Starting phenix.real_space_refine (version: dev) on Wed Apr 13 21:20:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a9z_6396/04_2022/5a9z_6396_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a9z_6396/04_2022/5a9z_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_6396/04_2022/5a9z_6396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a9z_6396/04_2022/5a9z_6396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a9z_6396/04_2022/5a9z_6396_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a9z_6396/04_2022/5a9z_6396_updated.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Convert atoms to be neutral 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'rna2p_pyr': 46, 'rna3p_pyr': 1153, 'p5*END': 1, 'rna3p_pur': 1590, 'rna2p_pur': 100} Link IDs: {'rna3p': 2742, 'rna2p': 146} 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: {'rna2p_pyr': 1, 'rna3p_pyr': 54, 'p5*END': 1, 'rna3p_pur': 67, 'rna2p_pur': 1} Link IDs: {'rna3p': 121, 'rna2p': 1} 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: {'PTRANS': 8, 'TRANS': 172, 'PCIS': 1} Chain: "AH" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1328 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 15, 'TRANS': 157, 'PCIS': 1} 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: {'rna3p_pyr': 632, 'rna2p_pur': 51, 'rna3p_pur': 804, 'rna2p_pyr': 28} Link IDs: {'rna3p': 1435, 'rna2p': 79} 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: {'PTRANS': 4, 'CIS': 2, '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: 61.48, per 1000 atoms: 0.41 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: 72.76 Conformation dependent library (CDL) restraints added in 6.3 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... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 188 helices and 75 sheets defined 35.6% alpha, 15.6% beta 1290 base pairs and 1336 stacking pairs defined. Time for finding SS restraints: 61.59 Creating SS restraints... Processing helix chain 'AC' and resid 7 through 15 removed outlier: 4.272A pdb=" N ASPAC 15 " --> pdb=" O LEUAC 11 " (cutoff:3.500A) Processing helix chain 'AC' and resid 22 through 33 Processing helix chain 'AC' and resid 79 through 90 Processing helix chain 'AC' and resid 96 through 106 Processing helix chain 'AC' and resid 119 through 126 Processing helix chain 'AC' and resid 127 through 132 Processing helix chain 'AC' and resid 148 through 159 Processing helix chain 'AC' and resid 181 through 200 Processing helix chain 'AD' and resid 132 through 137 removed outlier: 4.172A pdb=" N ILEAD 136 " --> pdb=" O PROAD 132 " (cutoff:3.500A) Proline residue: AD 137 - end of helix No H-bonds generated for 'chain 'AD' and resid 132 through 137' Processing helix chain 'AD' and resid 198 through 204 removed outlier: 5.950A pdb=" N LYSAD 202 " --> pdb=" O ASNAD 198 " (cutoff:3.500A) Processing helix chain 'AD' and resid 208 through 217 Processing helix chain 'AD' and resid 261 through 267 Proline residue: AD 265 - end of helix No H-bonds generated for 'chain 'AD' and resid 261 through 267' Processing helix chain 'AE' and resid 59 through 70 removed outlier: 4.941A pdb=" N LYSAE 69 " --> pdb=" O GLYAE 65 " (cutoff:3.500A) Processing helix chain 'AE' and resid 115 through 120 removed outlier: 4.367A pdb=" N TRPAE 120 " --> pdb=" O GLYAE 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'AE' and resid 115 through 120' Processing helix chain 'AF' and resid 23 through 30 removed outlier: 4.983A pdb=" N GLUAF 27 " --> pdb=" O ASPAF 23 " (cutoff:3.500A) Proline residue: AF 30 - end of helix Processing helix chain 'AF' and resid 31 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 168 removed outlier: 4.026A pdb=" N ARGAF 168 " --> pdb=" O ARGAF 164 " (cutoff:3.500A) Processing helix chain 'AF' and resid 182 through 189 Processing helix chain 'AF' and resid 196 through 210 Processing helix chain 'AF' and resid 52 through 58 removed outlier: 6.315A pdb=" N GLYAF 55 " --> pdb=" O LYSAF 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLUAF 56 " --> pdb=" O THRAF 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VALAF 57 " --> pdb=" O ARGAF 54 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALAAF 58 " --> pdb=" O GLYAF 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'AF' and resid 52 through 58' Processing helix chain 'AG' and resid 1 through 24 Proline residue: AG 17 - end of helix Processing helix chain 'AG' and resid 43 through 48 removed outlier: 4.438A pdb=" N LYSAG 47 " --> pdb=" O LEUAG 43 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLUAG 48 " --> pdb=" O GLYAG 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'AG' and resid 43 through 48' Processing helix chain 'AG' and resid 50 through 64 Processing helix chain 'AG' and resid 96 through 106 Processing helix chain 'AG' and resid 165 through 177 Processing helix chain 'AH' and resid 58 through 82 removed outlier: 3.790A pdb=" N GLYAH 82 " --> pdb=" O GLYAH 78 " (cutoff:3.500A) Processing helix chain 'AH' and resid 137 through 153 removed outlier: 4.637A pdb=" N ARGAH 152 " --> pdb=" O ILEAH 148 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYSAH 153 " --> pdb=" O ARGAH 149 " (cutoff:3.500A) Processing helix chain 'AI' and resid 9 through 20 removed outlier: 6.144A pdb=" N LEUAI 13 " --> pdb=" O LEUAI 9 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLUAI 15 " --> pdb=" O ALAAI 11 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASNAI 16 " --> pdb=" O THRAI 12 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLUAI 18 " --> pdb=" O LYSAI 14 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALAAI 20 " --> pdb=" O ASNAI 16 " (cutoff:3.500A) Processing helix chain 'AI' and resid 33 through 48 removed outlier: 3.783A pdb=" N LEUAI 40 " --> pdb=" O GLUAI 36 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEUAI 44 " --> pdb=" O LEUAI 40 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYSAI 45 " --> pdb=" O ARGAI 41 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLNAI 46 " --> pdb=" O GLNAI 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASNAI 47 " --> pdb=" O ALAAI 43 " (cutoff:3.500A) Processing helix chain 'AI' and resid 59 through 70 removed outlier: 5.734A pdb=" N LEUAI 63 " --> pdb=" O ILEAI 59 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEUAI 66 " --> pdb=" O ALAAI 62 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLYAI 67 " --> pdb=" O LEUAI 63 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEUAI 68 " --> pdb=" O LYSAI 64 " (cutoff:3.500A) Proline residue: AI 69 - end of helix Processing helix chain 'AI' and resid 86 through 91 removed outlier: 4.885A pdb=" N ALAAI 90 " --> pdb=" O PROAI 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYSAI 91 " --> pdb=" O VALAI 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'AI' and resid 86 through 91' Processing helix chain 'AI' and resid 94 through 107 removed outlier: 4.645A pdb=" N LYSAI 98 " --> pdb=" O VALAI 94 " (cutoff:3.500A) Proline residue: AI 101 - end of helix Proline residue: AI 105 - end of helix Processing helix chain 'AI' and resid 124 through 132 Proline residue: AI 129 - end of helix removed outlier: 4.518A pdb=" N ASPAI 132 " --> pdb=" O LEUAI 128 " (cutoff:3.500A) Processing helix chain 'AI' and resid 137 through 150 removed outlier: 3.793A pdb=" N GLNAI 143 " --> pdb=" O VALAI 139 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALAAI 144 " --> pdb=" O GLYAI 140 " (cutoff:3.500A) Proline residue: AI 145 - end of helix removed outlier: 3.674A pdb=" N LEUAI 149 " --> pdb=" O PROAI 145 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VALAI 150 " --> pdb=" O METAI 146 " (cutoff:3.500A) Processing helix chain 'AI' and resid 151 through 156 removed outlier: 4.005A pdb=" N GLYAI 155 " --> pdb=" O GLYAI 151 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 24 through 29 removed outlier: 4.368A pdb=" N GLNAJ 29 " --> pdb=" O PROAJ 25 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 36 through 45 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 80 Processing helix chain 'AJ' and resid 100 through 111 removed outlier: 4.262A pdb=" N LEUAJ 105 " --> pdb=" O TRPAJ 101 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALAAJ 108 " --> pdb=" O VALAJ 104 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLNAJ 110 " --> pdb=" O GLUAJ 106 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYSAJ 111 " --> pdb=" O ILEAJ 107 " (cutoff:3.500A) 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 'AJ' and resid 84 through 89 removed outlier: 4.702A pdb=" N GLYAJ 87 " --> pdb=" O LEUAJ 84 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALAAJ 88 " --> pdb=" O GLUAJ 85 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N HISAJ 89 " --> pdb=" O LYSAJ 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'AJ' and resid 84 through 89' Processing helix chain 'AK' and resid 23 through 36 removed outlier: 4.301A pdb=" N ARGAK 35 " --> pdb=" O ALAAK 31 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLYAK 36 " --> pdb=" O THRAK 32 " (cutoff:3.500A) Processing helix chain 'AK' and resid 86 through 94 Processing helix chain 'AK' and resid 95 through 108 Proline residue: AK 108 - end of helix Processing helix chain 'AK' and resid 110 through 121 removed outlier: 4.230A pdb=" N LYSAK 121 " --> pdb=" O PHEAK 117 " (cutoff:3.500A) Processing helix chain 'AK' and resid 127 through 134 removed outlier: 4.122A pdb=" N ARGAK 134 " --> pdb=" O HISAK 130 " (cutoff:3.500A) Processing helix chain 'AL' and resid 102 through 108 removed outlier: 4.646A pdb=" N LEUAL 106 " --> pdb=" O VALAL 102 " (cutoff:3.500A) Processing helix chain 'AL' and resid 111 through 119 Proline residue: AL 119 - end of helix 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 83 Processing helix chain 'AM' and resid 92 through 97 Proline residue: AM 97 - end of helix Processing helix chain 'AM' and resid 99 through 104 removed outlier: 3.552A pdb=" N ALAAM 103 " --> pdb=" O LEUAM 99 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLYAM 104 " --> pdb=" O LEUAM 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'AM' and resid 99 through 104' Processing helix chain 'AM' and resid 131 through 142 Processing helix chain 'AN' and resid 43 through 59 removed outlier: 4.830A pdb=" N ARGAN 59 " --> pdb=" O VALAN 55 " (cutoff:3.500A) Processing helix chain 'AN' and resid 111 through 126 Proline residue: AN 126 - end of helix 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 88 removed outlier: 4.388A pdb=" N ALAAO 84 " --> pdb=" O PHEAO 80 " (cutoff:3.500A) Proline residue: AO 85 - end of helix Processing helix chain 'AP' and resid 3 through 21 removed outlier: 4.891A pdb=" N THRAP 21 " --> pdb=" O ARGAP 17 " (cutoff:3.500A) Processing helix chain 'AP' and resid 63 through 82 removed outlier: 4.507A pdb=" N ILEAP 82 " --> pdb=" O LEUAP 78 " (cutoff:3.500A) Processing helix chain 'AP' and resid 96 through 111 Processing helix chain 'AQ' and resid 5 through 16 Processing helix chain 'AQ' and resid 103 through 108 Processing helix chain 'AQ' and resid 110 through 117 Processing helix chain 'AR' and resid 6 through 22 removed outlier: 4.786A pdb=" N LYSAR 22 " --> pdb=" O LEUAR 18 " (cutoff:3.500A) Processing helix chain 'AR' and resid 26 through 31 removed outlier: 6.962A pdb=" N LYSAR 30 " --> pdb=" O GLYAR 26 " (cutoff:3.500A) Processing helix chain 'AR' and resid 32 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 77 through 87 removed outlier: 4.805A pdb=" N GLYAR 87 " --> pdb=" O LEUAR 83 " (cutoff:3.500A) Processing helix chain 'AR' and resid 91 through 102 removed outlier: 5.167A pdb=" N LEUAR 95 " --> pdb=" O ASPAR 91 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALAAR 96 " --> pdb=" O ARGAR 92 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASPAR 97 " --> pdb=" O LYSAR 93 " (cutoff:3.500A) Processing helix chain 'AR' and resid 103 through 118 Processing helix chain 'AS' and resid 26 through 31 removed outlier: 5.494A pdb=" N GLYAS 30 " --> pdb=" O ASPAS 26 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALAAS 31 " --> pdb=" O ALAAS 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'AS' and resid 26 through 31' Processing helix chain 'AS' and resid 50 through 57 Processing helix chain 'AT' and resid 14 through 25 Processing helix chain 'AT' and resid 28 through 38 Processing helix chain 'AT' and resid 43 through 61 Processing helix chain 'AU' and resid 15 through 24 removed outlier: 4.206A pdb=" N ALAAU 19 " --> pdb=" O GLUAU 15 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLYAU 20 " --> pdb=" O LYSAU 16 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHEAU 21 " --> pdb=" O ALAAU 17 " (cutoff:3.500A) Processing helix chain 'AU' and resid 35 through 46 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 'AY' and resid 1 through 12 removed outlier: 5.592A pdb=" N SERAY 12 " --> pdb=" O ALAAY 8 " (cutoff:3.500A) Processing helix chain 'AY' and resid 13 through 34 Processing helix chain 'AY' and resid 37 through 67 removed outlier: 5.918A pdb=" N GLNAY 41 " --> pdb=" O GLYAY 37 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N HISAY 43 " --> pdb=" O LEUAY 39 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYSAY 44 " --> pdb=" O SERAY 40 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILEAY 45 " --> pdb=" O GLNAY 41 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 16 through 27 Processing helix chain 'AZ' and resid 40 through 51 Processing helix chain 'Aa' and resid 58 through 71 Processing helix chain 'Ab' and resid 12 through 24 Processing helix chain 'Ad' and resid 8 through 17 removed outlier: 4.259A pdb=" N GLYAd 17 " --> pdb=" O ALAAd 13 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 18 through 25 Proline residue: Ad 25 - end of helix Processing helix chain 'Ad' and resid 26 through 36 Processing helix chain 'Ad' and resid 42 through 47 Processing helix chain 'Ae' and resid 6 through 13 removed outlier: 4.400A pdb=" N ARGAe 13 " --> pdb=" O GLYAe 9 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 37 through 42 removed outlier: 5.040A pdb=" N ILEAe 41 " --> pdb=" O SERAe 37 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARGAe 42 " --> pdb=" O GLYAe 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ae' and resid 37 through 42' Processing helix chain 'Ae' and resid 52 through 61 removed outlier: 4.536A pdb=" N GLUAe 56 " --> pdb=" O LYSAe 52 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARGAe 57 " --> pdb=" O PROAe 53 " (cutoff:3.500A) Processing helix chain 'BF' and resid 44 through 65 Processing helix chain 'BF' and resid 77 through 89 Processing helix chain 'BF' and resid 100 through 105 removed outlier: 3.900A pdb=" N ASNBF 104 " --> pdb=" O GLYBF 100 " (cutoff:3.500A) Processing helix chain 'BF' and resid 106 through 122 removed outlier: 3.949A pdb=" N GLNBF 110 " --> pdb=" O LYSBF 106 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHEBF 122 " --> pdb=" O LEUBF 118 " (cutoff:3.500A) Processing helix chain 'BF' and resid 131 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 166 through 171 Processing helix chain 'BF' and resid 172 through 181 Processing helix chain 'BF' and resid 207 through 227 Processing helix chain 'BG' and resid 6 through 12 removed outlier: 4.002A pdb=" N ARGBG 11 " --> pdb=" O PROBG 7 " (cutoff:3.500A) Processing helix chain 'BG' and resid 28 through 48 Processing helix chain 'BG' and resid 72 through 77 removed outlier: 3.623A pdb=" N VALBG 76 " --> pdb=" O LYSBG 72 " (cutoff:3.500A) Processing helix chain 'BG' and resid 81 through 96 removed outlier: 3.917A pdb=" N ARGBG 85 " --> pdb=" O GLYBG 81 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VALBG 86 " --> pdb=" O GLUBG 82 " (cutoff:3.500A) 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) removed outlier: 4.478A pdb=" N THRBG 95 " --> pdb=" O LEUBG 91 " (cutoff:3.500A) Processing helix chain 'BG' and resid 108 through 113 removed outlier: 3.691A pdb=" N SERBG 112 " --> pdb=" O ASNBG 108 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALABG 113 " --> pdb=" O PROBG 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'BG' and resid 108 through 113' Processing helix chain 'BG' and resid 114 through 127 Processing helix chain 'BG' and resid 129 through 146 removed outlier: 5.579A pdb=" N GLYBG 145 " --> pdb=" O VALBG 141 " (cutoff:3.500A) Processing helix chain 'BH' and resid 7 through 16 removed outlier: 4.018A pdb=" N LEUBH 11 " --> pdb=" O PROBH 7 " (cutoff:3.500A) Processing helix chain 'BH' and resid 23 through 29 removed outlier: 6.199A pdb=" N TYRBH 27 " --> pdb=" O GLYBH 23 " (cutoff:3.500A) Proline residue: BH 29 - end of helix Processing helix chain 'BH' and resid 52 through 69 removed outlier: 4.002A pdb=" N TYRBH 68 " --> pdb=" O LEUBH 64 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLYBH 69 " --> pdb=" O ARGBH 65 " (cutoff:3.500A) Processing helix chain 'BH' and resid 71 through 86 removed outlier: 4.242A pdb=" N LYSBH 86 " --> pdb=" O ALABH 82 " (cutoff:3.500A) Processing helix chain 'BH' and resid 88 through 100 removed outlier: 3.508A pdb=" N ARGBH 100 " --> pdb=" O LEUBH 96 " (cutoff:3.500A) Processing helix chain 'BH' and resid 101 through 109 removed outlier: 5.325A pdb=" N GLYBH 109 " --> pdb=" O VALBH 105 " (cutoff:3.500A) Processing helix chain 'BH' and resid 113 through 124 Processing helix chain 'BH' and resid 155 through 166 Processing helix chain 'BH' and resid 190 through 195 removed outlier: 4.011A pdb=" N LEUBH 194 " --> pdb=" O ASPBH 190 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ALABH 195 " --> pdb=" O ARGBH 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'BH' and resid 190 through 195' Processing helix chain 'BH' and resid 199 through 208 removed outlier: 6.956A pdb=" N VALBH 203 " --> pdb=" O ASNBH 199 " (cutoff:3.500A) Processing helix chain 'BI' and resid 50 through 66 Processing helix chain 'BI' and resid 103 through 114 Processing helix chain 'BI' and resid 127 through 142 removed outlier: 4.627A pdb=" N LEUBI 142 " --> pdb=" O ALABI 138 " (cutoff:3.500A) Processing helix chain 'BI' and resid 144 through 153 Processing helix chain 'BJ' and resid 16 through 34 Processing helix chain 'BJ' and resid 70 through 83 removed outlier: 4.205A pdb=" N ASPBJ 74 " --> pdb=" O ASPBJ 70 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARGBJ 82 " --> pdb=" O GLUBJ 78 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASPBJ 83 " --> pdb=" O LEUBJ 79 " (cutoff:3.500A) Processing helix chain 'BK' and resid 20 through 32 removed outlier: 4.779A pdb=" N ARGBK 32 " --> pdb=" O ASNBK 28 " (cutoff:3.500A) Processing helix chain 'BK' and resid 35 through 53 Processing helix chain 'BK' and resid 57 through 70 Processing helix chain 'BK' and resid 92 through 112 Proline residue: BK 112 - end of helix Processing helix chain 'BK' and resid 115 through 130 Processing helix chain 'BK' and resid 133 through 153 removed outlier: 4.078A pdb=" N GLUBK 146 " --> pdb=" O GLUBK 142 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALABK 147 " --> pdb=" O ARGBK 143 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASNBK 148 " --> pdb=" O METBK 144 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARGBK 149 " --> pdb=" O ALABK 145 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALABK 150 " --> pdb=" O GLUBK 146 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYRBK 151 " --> pdb=" O ALABK 147 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HISBK 153 " --> pdb=" O ARGBK 149 " (cutoff:3.500A) Processing helix chain 'BL' and resid 4 through 20 removed outlier: 4.415A pdb=" N VALBL 19 " --> pdb=" O ASNBL 15 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYRBL 20 " --> pdb=" O ALABL 16 " (cutoff:3.500A) Processing helix chain 'BL' and resid 29 through 43 Processing helix chain 'BL' and resid 121 through 128 Processing helix chain 'BM' and resid 32 through 38 removed outlier: 4.405A pdb=" N GLNBM 38 " --> pdb=" O ASNBM 34 " (cutoff:3.500A) Processing helix chain 'BM' and resid 40 through 54 removed outlier: 4.964A pdb=" N VALBM 44 " --> pdb=" O LEUBM 40 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALABM 45 " --> pdb=" O VALBM 41 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALABM 46 " --> pdb=" O ARGBM 42 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEUBM 47 " --> pdb=" O ALABM 43 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLUBM 48 " --> pdb=" O VALBM 44 " (cutoff:3.500A) Proline residue: BM 49 - end of helix removed outlier: 5.029A pdb=" N VALBM 53 " --> pdb=" O PROBM 49 " (cutoff:3.500A) Processing helix chain 'BM' and resid 70 through 90 Proline residue: BM 90 - end of helix Processing helix chain 'BM' and resid 92 through 97 removed outlier: 4.376A pdb=" N LYSBM 97 " --> pdb=" O TYRBM 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'BM' and resid 92 through 97' Processing helix chain 'BN' and resid 12 through 28 removed outlier: 3.783A pdb=" N LEUBN 16 " --> pdb=" O ASPBN 12 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASPBN 17 " --> pdb=" O HISBN 13 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARGBN 28 " --> pdb=" O VALBN 24 " (cutoff:3.500A) Processing helix chain 'BN' and resid 80 through 86 removed outlier: 4.085A pdb=" N GLNBN 84 " --> pdb=" O LYSBN 80 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEUBN 85 " --> pdb=" O THRBN 81 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N METBN 86 " --> pdb=" O ILEBN 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'BN' and resid 80 through 86' Processing helix chain 'BO' and resid 44 through 49 removed outlier: 4.957A pdb=" N GLYBO 49 " --> pdb=" O GLYBO 45 " (cutoff:3.500A) Processing helix chain 'BO' and resid 53 through 58 removed outlier: 6.166A pdb=" N THRBO 57 " --> pdb=" O SERBO 53 " (cutoff:3.500A) Proline residue: BO 58 - end of helix No H-bonds generated for 'chain 'BO' and resid 53 through 58' Processing helix chain 'BO' and resid 59 through 76 removed outlier: 4.809A pdb=" N GLYBO 76 " --> pdb=" O ALABO 72 " (cutoff:3.500A) Processing helix chain 'BO' and resid 90 through 102 Processing helix chain 'BO' and resid 122 through 127 removed outlier: 3.626A pdb=" N ARGBO 126 " --> pdb=" O LYSBO 122 " (cutoff:3.500A) Processing helix chain 'BP' and resid 7 through 14 Processing helix chain 'BQ' and resid 14 through 23 removed outlier: 4.325A pdb=" N TYRBQ 21 " --> pdb=" O VALBQ 17 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILEBQ 22 " --> pdb=" O ALABQ 18 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYRBQ 23 " --> pdb=" O LEUBQ 19 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 27 through 38 removed outlier: 6.246A pdb=" N LYSBQ 31 " --> pdb=" O LYSBQ 27 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLUBQ 32 " --> pdb=" O ALABQ 28 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 51 through 64 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) removed outlier: 4.095A pdb=" N THRBQ 63 " --> pdb=" O TYRBQ 59 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TRPBQ 64 " --> pdb=" O VALBQ 60 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 69 through 85 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) removed outlier: 5.122A pdb=" N GLYBQ 85 " --> pdb=" O LEUBQ 81 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 86 through 95 removed outlier: 4.954A pdb=" N LEUBQ 90 " --> pdb=" O CYSBQ 86 " (cutoff:3.500A) 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) removed outlier: 4.417A pdb=" N GLYBQ 95 " --> pdb=" O ARGBQ 91 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 107 through 112 Processing helix chain 'BR' and resid 3 through 8 removed outlier: 4.220A pdb=" N ILEBR 7 " --> pdb=" O ARGBR 3 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLUBR 8 " --> pdb=" O LYSBR 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'BR' and resid 3 through 8' Processing helix chain 'BR' and resid 40 through 51 Processing helix chain 'BS' and resid 4 through 16 Processing helix chain 'BS' and resid 24 through 47 removed outlier: 3.820A pdb=" N HISBS 46 " --> pdb=" O HISBS 42 " (cutoff:3.500A) Processing helix chain 'BS' and resid 49 through 74 Processing helix chain 'BS' and resid 75 through 86 Processing helix chain 'BT' and resid 52 through 62 removed outlier: 4.465A pdb=" N VALBT 62 " --> pdb=" O TYRBT 58 " (cutoff:3.500A) Processing helix chain 'BT' and resid 67 through 78 Processing helix chain 'BU' and resid 81 through 98 removed outlier: 4.284A pdb=" N VALBU 85 " --> pdb=" O ARGBU 81 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLNBU 96 " --> pdb=" O ARGBU 92 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SERBU 97 " --> pdb=" O GLNBU 93 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEUBU 98 " --> pdb=" O ASNBU 94 " (cutoff:3.500A) Processing helix chain 'BV' and resid 36 through 45 removed outlier: 4.400A pdb=" N PHEBV 43 " --> pdb=" O VALBV 39 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEUBV 44 " --> pdb=" O LEUBV 40 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SERBV 45 " --> pdb=" O LYSBV 41 " (cutoff:3.500A) Processing helix chain 'BV' and resid 52 through 57 Processing helix chain 'BV' and resid 59 through 77 Processing helix chain 'BW' and resid 12 through 26 removed outlier: 5.111A pdb=" N LEUBW 16 " --> pdb=" O ASPBW 12 " (cutoff:3.500A) 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) removed outlier: 4.747A pdb=" N ALABW 24 " --> pdb=" O LEUBW 20 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYSBW 25 " --> pdb=" O GLUBW 21 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLYBW 26 " --> pdb=" O LEUBW 22 " (cutoff:3.500A) Processing helix chain 'BW' and resid 70 through 76 removed outlier: 4.722A pdb=" N PHEBW 74 " --> pdb=" O LYSBW 70 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALABW 75 " --> pdb=" O LEUBW 71 " (cutoff:3.500A) Proline residue: BW 76 - end of helix No H-bonds generated for 'chain 'BW' and resid 70 through 76' Processing helix chain 'BX' and resid 12 through 47 removed outlier: 3.987A pdb=" N HISBX 16 " --> pdb=" O ALABX 12 " (cutoff:3.500A) Processing helix chain 'BX' and resid 48 through 70 removed outlier: 4.113A pdb=" N GLYBX 69 " --> pdb=" O LYSBX 65 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SERBX 70 " --> pdb=" O ALABX 66 " (cutoff:3.500A) Processing helix chain 'BX' and resid 75 through 94 removed outlier: 4.589A pdb=" N ALABX 94 " --> pdb=" O GLNBX 90 " (cutoff:3.500A) Processing helix chain 'BY' and resid 8 through 16 Processing helix chain 'CA' and resid 17 through 30 removed outlier: 4.051A pdb=" N LEUCA 21 " --> pdb=" O GLYCA 17 " (cutoff:3.500A) 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) removed outlier: 7.642A pdb=" N GLNCA 27 " --> pdb=" O ASPCA 23 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLNCA 28 " --> pdb=" O LYSCA 24 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SERCA 29 " --> pdb=" O LEUCA 25 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLYCA 30 " --> pdb=" O LEUCA 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'CA' and resid 17 through 30' Processing helix chain 'CA' and resid 85 through 92 removed outlier: 3.543A pdb=" N METCA 89 " --> pdb=" O VALCA 85 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N METCA 91 " --> pdb=" O ARGCA 87 " (cutoff:3.500A) Processing helix chain 'CA' and resid 106 through 118 removed outlier: 3.546A pdb=" N ARGCA 110 " --> pdb=" O METCA 106 " (cutoff:3.500A) 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 136 through 152 removed outlier: 3.840A pdb=" N VALCA 140 " --> pdb=" O ARGCA 136 " (cutoff:3.500A) 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) removed outlier: 4.874A pdb=" N PHECA 148 " --> pdb=" O VALCA 144 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VALCA 149 " --> pdb=" O PHECA 145 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASNCA 150 " --> pdb=" O ASPCA 146 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEUCA 151 " --> pdb=" O LEUCA 147 " (cutoff:3.500A) Processing helix chain 'CA' and resid 155 through 160 removed outlier: 4.517A pdb=" N ASPCA 159 " --> pdb=" O ASPCA 155 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHECA 160 " --> pdb=" O GLUCA 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'CA' and resid 155 through 160' Processing helix chain 'CA' and resid 178 through 183 removed outlier: 5.300A pdb=" N ASPCA 182 " --> pdb=" O ASPCA 178 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N METCA 183 " --> pdb=" O METCA 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'CA' and resid 178 through 183' Processing helix chain 'CA' and resid 184 through 194 removed outlier: 4.217A pdb=" N GLNCA 188 " --> pdb=" O THRCA 184 " (cutoff:3.500A) Processing helix chain 'CA' and resid 327 through 342 removed outlier: 3.625A pdb=" N ILECA 331 " --> pdb=" O THRCA 327 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VALCA 340 " --> pdb=" O ASNCA 336 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N HISCA 341 " --> pdb=" O LYSCA 337 " (cutoff:3.500A) Processing helix chain 'CA' and resid 362 through 377 removed outlier: 3.519A pdb=" N LEUCA 369 " --> pdb=" O HISCA 365 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILECA 370 " --> pdb=" O LEUCA 366 " (cutoff:3.500A) Processing helix chain 'CA' and resid 408 through 423 removed outlier: 4.565A pdb=" N GLNCA 412 " --> pdb=" O GLUCA 408 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLYCA 413 " --> pdb=" O GLUCA 409 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SERCA 414 " --> pdb=" O GLNCA 410 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N METCA 416 " --> pdb=" O GLNCA 412 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNCA 417 " --> pdb=" O GLYCA 413 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALACA 418 " --> pdb=" O SERCA 414 " (cutoff:3.500A) Processing helix chain 'CA' and resid 444 through 449 removed outlier: 4.070A pdb=" N ILECA 449 " --> pdb=" O SERCA 445 " (cutoff:3.500A) Processing helix chain 'CA' and resid 450 through 460 Processing helix chain 'CA' and resid 497 through 508 removed outlier: 5.221A pdb=" N GLYCA 503 " --> pdb=" O PHECA 499 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEUCA 504 " --> pdb=" O ALACA 500 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASPCA 506 " --> pdb=" O PHECA 502 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARGCA 507 " --> pdb=" O GLYCA 503 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLYCA 508 " --> pdb=" O LEUCA 504 " (cutoff:3.500A) Processing helix chain 'CA' and resid 564 through 572 Processing helix chain 'CA' and resid 593 through 602 removed outlier: 3.564A pdb=" N ARGCA 598 " --> pdb=" O GLUCA 594 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARGCA 599 " --> pdb=" O ASNCA 595 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALACA 600 " --> pdb=" O ASPCA 596 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'AC' and resid 92 through 95 Processing sheet with id= 2, first strand: chain 'AC' and resid 169 through 174 removed outlier: 5.673A pdb=" N GLYAC 169 " --> pdb=" O LEUAC 47 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THRAC 40 " --> pdb=" O THRAC 217 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THRAC 217 " --> pdb=" O THRAC 40 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'AD' and resid 5 through 9 removed outlier: 5.962A pdb=" N PHEAD 6 " --> pdb=" O THRAD 27 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'AD' and resid 80 through 84 removed outlier: 4.250A pdb=" N GLUAD 101 " --> pdb=" O TYRAD 97 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'AD' and resid 117 through 120 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'AD' and resid 144 through 147 removed outlier: 5.100A pdb=" N ALAAD 144 " --> pdb=" O THRAD 192 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N THRAD 192 " --> pdb=" O ALAAD 144 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'AD' and resid 166 through 169 removed outlier: 3.580A pdb=" N GLUAD 181 " --> pdb=" O LEUAD 177 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'AE' and resid 1 through 5 removed outlier: 5.941A pdb=" N METAE 1 " --> pdb=" O GLUAE 200 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLUAE 163 " --> pdb=" O SERAE 108 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'AE' and resid 9 through 14 removed outlier: 3.877A pdb=" N VALAE 9 " --> pdb=" O THRAE 24 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VALAE 23 " --> pdb=" O VALAE 184 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASNAE 180 " --> pdb=" O LEUAE 27 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'AE' and resid 33 through 37 removed outlier: 6.897A pdb=" N ARGAE 76 " --> pdb=" O GLYAE 50 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'AF' and resid 6 through 11 Processing sheet with id= 12, first strand: chain 'AF' and resid 172 through 176 Processing sheet with id= 13, first strand: chain 'AG' and resid 34 through 41 removed outlier: 6.923A pdb=" N LEUAG 34 " --> pdb=" O THRAG 162 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THRAG 162 " --> pdb=" O LEUAG 34 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYSAG 36 " --> pdb=" O VALAG 160 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'AH' and resid 7 through 10 removed outlier: 5.180A pdb=" N LEUAH 7 " --> pdb=" O VALAH 52 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARGAH 42 " --> pdb=" O GLUAH 53 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'AH' and resid 16 through 19 Processing sheet with id= 16, first strand: chain 'AH' and resid 83 through 89 removed outlier: 4.154A pdb=" N TYRAH 83 " --> pdb=" O GLYAH 135 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEUAH 87 " --> pdb=" O VALAH 131 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THRAH 129 " --> pdb=" O ILEAH 89 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'AH' and resid 94 through 97 removed outlier: 6.391A pdb=" N ARGAH 97 " --> pdb=" O GLUAH 104 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'AI' and resid 82 through 85 removed outlier: 5.561A pdb=" N VALAI 27 " --> pdb=" O TYRAI 83 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHEAI 24 " --> pdb=" O LEUAI 117 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLNAI 115 " --> pdb=" O LEUAI 26 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'AK' and resid 13 through 17 Processing sheet with id= 20, first strand: chain 'AK' and resid 71 through 74 removed outlier: 4.009A pdb=" N LYSAK 83 " --> pdb=" O THRAK 73 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'AL' and resid 5 through 10 removed outlier: 6.405A pdb=" N ARGAL 17 " --> pdb=" O VALAL 10 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'AL' and resid 38 through 42 Processing sheet with id= 23, first strand: chain 'AL' and resid 68 through 71 removed outlier: 3.792A pdb=" N GLYAL 74 " --> pdb=" O LYSAL 70 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'AN' and resid 32 through 37 removed outlier: 4.363A pdb=" N TYRAN 32 " --> pdb=" O GLUAN 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARGAN 101 " --> pdb=" O ALAAN 36 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VALAN 106 " --> pdb=" O ILEAN 64 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILEAN 64 " --> pdb=" O VALAN 106 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'AN' and resid 71 through 74 Processing sheet with id= 26, first strand: chain 'AO' and resid 33 through 37 removed outlier: 6.515A pdb=" N LEUAO 111 " --> pdb=" O LEUAO 100 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'AP' and resid 24 through 31 removed outlier: 3.874A pdb=" N PHEAP 29 " --> pdb=" O TYRAP 36 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TYRAP 36 " --> pdb=" O PHEAP 29 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SERAP 31 " --> pdb=" O HISAP 34 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HISAP 34 " --> pdb=" O SERAP 31 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'AQ' and resid 47 through 51 Processing sheet with id= 29, first strand: chain 'AQ' and resid 53 through 58 removed outlier: 6.976A pdb=" N PHEAQ 61 " --> pdb=" O SERAQ 80 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VALAQ 72 " --> pdb=" O VALAQ 70 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'AS' and resid 32 through 38 Processing sheet with id= 31, first strand: chain 'AS' and resid 73 through 79 removed outlier: 5.894A pdb=" N SERAS 73 " --> pdb=" O GLNAS 89 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'AT' and resid 2 through 8 removed outlier: 4.664A pdb=" N THRAT 100 " --> pdb=" O GLYAT 79 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALAAT 73 " --> pdb=" O ILEAT 106 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'AT' and resid 80 through 86 removed outlier: 3.650A pdb=" N ASPAT 94 " --> pdb=" O LEUAT 86 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'AU' and resid 25 through 29 removed outlier: 4.808A pdb=" N LYSAU 53 " --> pdb=" O GLNAU 82 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'AV' and resid 9 through 14 removed outlier: 7.586A pdb=" N GLYAV 10 " --> pdb=" O VALAV 24 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VALAV 24 " --> pdb=" O GLYAV 10 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THRAV 12 " --> pdb=" O GLYAV 22 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLYAV 22 " --> pdb=" O THRAV 12 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYRAV 20 " --> pdb=" O LEUAV 14 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'AV' and resid 27 through 30 removed outlier: 3.922A pdb=" N VALAV 27 " --> pdb=" O ALAAV 36 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LYSAV 34 " --> pdb=" O GLUAV 29 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'AW' and resid 34 through 40 removed outlier: 8.077A pdb=" N GLUAW 84 " --> pdb=" O LYSAW 23 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLNAW 73 " --> pdb=" O ASPAW 87 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'AW' and resid 58 through 61 Processing sheet with id= 39, first strand: chain 'AW' and resid 101 through 106 Processing sheet with id= 40, first strand: chain 'AW' and resid 115 through 121 removed outlier: 8.854A pdb=" N GLYAW 115 " --> pdb=" O PROAW 177 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILEAW 171 " --> pdb=" O HISAW 121 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASPAW 148 " --> pdb=" O VALAW 174 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'AX' and resid 37 through 40 removed outlier: 4.738A pdb=" N PHEAX 57 " --> pdb=" O GLNAX 40 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THRAX 58 " --> pdb=" O GLYAX 54 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'AX' and resid 66 through 71 Processing sheet with id= 43, first strand: chain 'AZ' and resid 33 through 38 removed outlier: 4.160A pdb=" N GLNAZ 33 " --> pdb=" O LEUAZ 8 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEUAZ 53 " --> pdb=" O VALAZ 9 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Aa' and resid 17 through 20 removed outlier: 6.004A pdb=" N PHEAa 42 " --> pdb=" O GLUAa 57 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLUAa 57 " --> pdb=" O PHEAa 42 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Ac' and resid 11 through 16 removed outlier: 6.583A pdb=" N GLUAc 12 " --> pdb=" O GLUAc 24 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLUAc 24 " --> pdb=" O GLUAc 12 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THRAc 14 " --> pdb=" O ALAAc 22 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASNAc 20 " --> pdb=" O CYSAc 16 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Ac' and resid 36 through 39 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'Af' and resid 14 through 18 Processing sheet with id= 48, first strand: chain 'BF' and resid 17 through 20 removed outlier: 6.726A pdb=" N PHEBF 17 " --> pdb=" O ILEBF 42 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HISBF 40 " --> pdb=" O HISBF 19 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'BF' and resid 90 through 93 Processing sheet with id= 50, first strand: chain 'BG' and resid 19 through 22 removed outlier: 5.516A pdb=" N GLUBG 19 " --> pdb=" O VALBG 55 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILEBG 57 " --> pdb=" O GLUBG 19 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLUBG 58 " --> pdb=" O ALABG 65 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'BG' and resid 164 through 170 removed outlier: 5.476A pdb=" N ARGBG 164 " --> pdb=" O GLYBG 155 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLYBG 148 " --> pdb=" O PHEBG 203 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEUBG 196 " --> pdb=" O ALABG 189 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALABG 189 " --> pdb=" O LEUBG 196 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASNBG 181 " --> pdb=" O LEUBG 204 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'BH' and resid 143 through 147 Processing sheet with id= 53, first strand: chain 'BI' and resid 6 through 11 removed outlier: 3.818A pdb=" N LEUBI 31 " --> pdb=" O ILEBI 11 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARGBI 40 " --> pdb=" O ASPBI 36 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'BI' and resid 79 through 83 removed outlier: 5.160A pdb=" N ASPBI 117 " --> pdb=" O ALABI 94 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'BJ' and resid 39 through 42 removed outlier: 5.242A pdb=" N TRPBJ 62 " --> pdb=" O GLUBJ 41 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BJ' and resid 45 through 48 Processing sheet with id= 57, first strand: chain 'BK' and resid 74 through 79 Processing sheet with id= 58, first strand: chain 'BL' and resid 22 through 26 removed outlier: 6.680A pdb=" N GLUBL 22 " --> pdb=" O LEUBL 63 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'BL' and resid 82 through 85 Processing sheet with id= 60, first strand: chain 'BM' and resid 3 through 9 removed outlier: 4.193A pdb=" N LYSBM 25 " --> pdb=" O PHEBM 59 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'BN' and resid 37 through 40 removed outlier: 4.435A pdb=" N ILEBN 38 " --> pdb=" O LEUBN 71 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEUBN 40 " --> pdb=" O ASNBN 69 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASNBN 69 " --> pdb=" O LEUBN 40 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VALBN 72 " --> pdb=" O ILEBN 6 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILEBN 6 " --> pdb=" O VALBN 72 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARGBN 9 " --> pdb=" O GLUBN 95 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLUBN 95 " --> pdb=" O ARGBN 9 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'BO' and resid 26 through 34 removed outlier: 4.946A pdb=" N ASNBO 27 " --> pdb=" O SERBO 24 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VALBO 105 " --> pdb=" O GLNBO 78 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VALBO 80 " --> pdb=" O VALBO 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SERBO 107 " --> pdb=" O VALBO 80 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'BP' and resid 32 through 36 Processing sheet with id= 64, first strand: chain 'BP' and resid 40 through 44 removed outlier: 3.862A pdb=" N ARGBP 41 " --> pdb=" O VALBP 55 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VALBP 55 " --> pdb=" O ARGBP 41 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYSBP 54 " --> pdb=" O ILEBP 70 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'BT' and resid 2 through 10 removed outlier: 5.976A pdb=" N ASPBT 40 " --> pdb=" O PROBT 15 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYRBT 17 " --> pdb=" O TYRBT 38 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYRBT 38 " --> pdb=" O TYRBT 17 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILEBT 19 " --> pdb=" O ILEBT 36 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'BU' and resid 7 through 11 removed outlier: 4.830A pdb=" N ASPBU 55 " --> pdb=" O VALBU 10 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'BW' and resid 46 through 52 removed outlier: 3.805A pdb=" N VALBW 58 " --> pdb=" O VALBW 51 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'CA' and resid 74 through 77 removed outlier: 3.651A pdb=" N THRCA 75 " --> pdb=" O ILECA 10 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLYCA 77 " --> pdb=" O ALACA 12 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILECA 11 " --> pdb=" O LEUCA 96 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VALCA 98 " --> pdb=" O ILECA 11 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HISCA 13 " --> pdb=" O VALCA 98 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N ASPCA 100 " --> pdb=" O HISCA 13 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYSCA 122 " --> pdb=" O ASPCA 93 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALACA 161 " --> pdb=" O PROCA 123 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VALCA 125 " --> pdb=" O ALACA 161 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'CA' and resid 210 through 215 removed outlier: 4.516A pdb=" N ILECA 223 " --> pdb=" O GLNCA 211 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'CA' and resid 235 through 239 removed outlier: 3.670A pdb=" N GLNCA 235 " --> pdb=" O ASNCA 248 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VALCA 237 " --> pdb=" O THRCA 246 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THRCA 246 " --> pdb=" O VALCA 237 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLYCA 244 " --> pdb=" O ILECA 239 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'CA' and resid 305 through 312 removed outlier: 6.241A pdb=" N ARGCA 361 " --> pdb=" O PROCA 305 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VALCA 307 " --> pdb=" O SERCA 359 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SERCA 359 " --> pdb=" O VALCA 307 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N METCA 309 " --> pdb=" O ARGCA 357 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARGCA 357 " --> pdb=" O METCA 309 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHECA 311 " --> pdb=" O ALACA 355 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALACA 355 " --> pdb=" O THRCA 350 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THRCA 350 " --> pdb=" O ALACA 355 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARGCA 361 " --> pdb=" O ALACA 344 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N ALACA 344 " --> pdb=" O ARGCA 361 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'CA' and resid 401 through 407 removed outlier: 4.999A pdb=" N GLUCA 401 " --> pdb=" O VALCA 442 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VALCA 442 " --> pdb=" O GLUCA 401 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VALCA 403 " --> pdb=" O ASPCA 440 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASPCA 440 " --> pdb=" O VALCA 403 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEUCA 405 " --> pdb=" O ARGCA 438 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARGCA 438 " --> pdb=" O LEUCA 405 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VALCA 407 " --> pdb=" O ARGCA 436 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASNCA 430 " --> pdb=" O ARGCA 438 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNCA 428 " --> pdb=" O ASPCA 440 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'CA' and resid 486 through 489 No H-bonds generated for sheet with id= 73 Processing sheet with id= 74, first strand: chain 'CA' and resid 492 through 495 No H-bonds generated for sheet with id= 74 Processing sheet with id= 75, first strand: chain 'CA' and resid 576 through 580 1847 hydrogen bonds defined for protein. 5472 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: 192.50 Time building geometry restraints manager: 78.95 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: 79194 35.99 - 71.97: 7526 71.97 - 107.96: 744 107.96 - 143.94: 172 143.94 - 179.93: 116 Dihedral angle restraints: 87752 sinusoidal: 68396 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 87749 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: 1546 1.96 - 2.94: 105833 2.94 - 3.92: 526219 3.92 - 4.90: 851486 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1485252 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 1485247 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 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. 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 15.840 Check model and map are aligned: 1.640 Convert atoms to be neutral: 0.960 Process input model: 501.320 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 527.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 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= 0.797 Angle : 1.890 82.556 242863 Z= 1.168 Chirality : 0.136 1.264 30675 Planarity : 0.027 0.362 13938 Dihedral : 23.313 179.927 75269 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 199.39 Ramachandran Plot: Outliers : 25.22 % Allowed : 25.13 % Favored : 49.64 % Rotamer Outliers : 29.15 % 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 *********************** 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 : 6.519 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: 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1569 outliers final: 572 residues processed: 3100 average time/residue: 1.6709 time to fit residues: 8664.3107 Evaluate side-chains 1950 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 572 poor density : 1378 time to evaluate : 6.801 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 572 outliers final: 68 residues processed: 572 average time/residue: 1.5213 time to fit residues: 1520.3003 ------------------------------------------------------------------------------- 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: 1.9990 chunk 838 optimal weight: 6.9990 chunk 465 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 565 optimal weight: 7.9990 chunk 447 optimal weight: 5.9990 chunk 866 optimal weight: 5.9990 chunk 335 optimal weight: 6.9990 chunk 527 optimal weight: 9.9990 chunk 645 optimal weight: 6.9990 chunk 1004 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 46 GLN ** AD 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 201 HIS AD 227 ASN ** AD 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 233 HIS ** AE 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 129 HIS AE 132 HIS AE 180 ASN ** AE 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 69 HIS ** AF 203 GLN ** 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** ** AH 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 30 HIS ** AK 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AL 88 ASN ** AM 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 89 ASN AO 31 HIS ** AR 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 81 HIS ** AR 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AT 57 ASN AT 60 ASN ** AT 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AU 82 GLN AU 87 GLN ** AV 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AV 43 ASN AW 32 HIS AX 3 HIS ** AY 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 51 GLN ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 31 HIS ** Ae 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 20 HIS ** 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** BF 212 GLN ** BG 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 104 GLN ** BG 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 110 ASN ** 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 77 ASN ** BH 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 7 ASN 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 97 GLN BK 109 ASN BK 110 GLN BL 70 GLN ** BL 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BM 38 GLN BM 73 GLN BN 68 HIS ** BO 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BP 99 HIS ** BQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 52 GLN ** BS 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 13 GLN BS 50 HIS ** BS 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BT 82 GLN BW 53 ASN ** BX 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.573 163075 Z= 0.431 Angle : 1.363 55.172 242863 Z= 0.673 Chirality : 0.064 1.901 30675 Planarity : 0.011 0.161 13938 Dihedral : 20.833 179.873 61967 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 46.93 Ramachandran Plot: Outliers : 6.28 % Allowed : 24.75 % Favored : 68.97 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.99 % Twisted Proline : 0.30 % Twisted General : 0.57 % 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: -6.45 (0.07), residues: 6565 helix: -3.51 (0.08), residues: 1880 sheet: -2.77 (0.16), residues: 850 loop : -5.38 (0.07), residues: 3835 *********************** 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 2016 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1856 time to evaluate : 6.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 160 outliers final: 60 residues processed: 1960 average time/residue: 1.5467 time to fit residues: 5128.8248 Evaluate side-chains 1347 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1287 time to evaluate : 6.783 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 60 outliers final: 8 residues processed: 60 average time/residue: 1.3369 time to fit residues: 151.9930 ------------------------------------------------------------------------------- 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: 5.9990 chunk 311 optimal weight: 20.0000 chunk 835 optimal weight: 5.9990 chunk 683 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 chunk 1006 optimal weight: 0.9980 chunk 1086 optimal weight: 0.9990 chunk 896 optimal weight: 6.9990 chunk 997 optimal weight: 30.0000 chunk 343 optimal weight: 2.9990 chunk 807 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 58 HIS ** 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 192 ASN ** AF 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 42 ASN AK 94 HIS AL 5 GLN ** AN 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 23 ASN AO 61 HIS ** AQ 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 44 ASN ** AR 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 11 GLN AS 89 GLN ** AT 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 60 ASN ** AW 65 GLN ** 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** ** Aa 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 47 GLN ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 26 ASN ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 40 HIS ** BF 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 161 ASN BI 78 HIS ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 153 HIS BL 82 HIS ** BN 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 28 GLN ** BS 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 45 GLN CA 28 GLN ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 234 ASN CA 341 HIS ** CA 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.565 163075 Z= 0.346 Angle : 1.074 41.279 242863 Z= 0.531 Chirality : 0.052 1.787 30675 Planarity : 0.009 0.121 13938 Dihedral : 19.935 179.570 61967 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 36.48 Ramachandran Plot: Outliers : 4.28 % Allowed : 22.65 % Favored : 73.07 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.95 % Twisted Proline : 0.90 % Twisted General : 0.57 % 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: -5.33 (0.08), residues: 6565 helix: -2.14 (0.10), residues: 1923 sheet: -2.43 (0.16), residues: 864 loop : -4.87 (0.08), residues: 3778 *********************** 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 1834 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1749 time to evaluate : 6.744 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 outliers start: 85 outliers final: 39 residues processed: 1808 average time/residue: 1.5460 time to fit residues: 4735.2361 Evaluate side-chains 1326 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1287 time to evaluate : 6.787 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 8 residues processed: 39 average time/residue: 1.2501 time to fit residues: 98.4646 ------------------------------------------------------------------------------- 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: 20.0000 chunk 756 optimal weight: 20.0000 chunk 522 optimal weight: 0.9990 chunk 111 optimal weight: 40.0000 chunk 480 optimal weight: 8.9990 chunk 675 optimal weight: 30.0000 chunk 1009 optimal weight: 40.0000 chunk 1069 optimal weight: 20.0000 chunk 527 optimal weight: 1.9990 chunk 957 optimal weight: 30.0000 chunk 288 optimal weight: 30.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 172 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 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 129 HIS ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 204 ASN ** 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 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 138 GLN AJ 11 GLN AJ 103 GLN AK 38 HIS ** AK 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 101 HIS ** AK 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AM 70 GLN ** AM 81 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** ** AP 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AW 54 HIS AW 55 HIS ** AW 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 35 ASN ** 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 51 GLN ** Aa 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 33 ASN ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 36 GLN ** BF 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 224 GLN ** BG 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 65 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** BK 84 ASN BM 73 GLN BN 68 HIS ** BO 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 92 HIS BS 13 GLN ** BV 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 23 ASN CA 208 GLN CA 234 ASN ** CA 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 411 HIS CA 514 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.9158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.562 163075 Z= 0.533 Angle : 1.309 40.844 242863 Z= 0.637 Chirality : 0.061 2.006 30675 Planarity : 0.012 0.279 13938 Dihedral : 20.607 179.986 61967 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 56.23 Ramachandran Plot: Outliers : 4.01 % Allowed : 22.50 % Favored : 73.50 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.94 % Twisted Proline : 1.50 % Twisted General : 1.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.08), residues: 6565 helix: -2.24 (0.10), residues: 1926 sheet: -2.73 (0.15), residues: 956 loop : -4.78 (0.08), residues: 3683 *********************** 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 1807 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1720 time to evaluate : 6.861 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 outliers start: 87 outliers final: 40 residues processed: 1777 average time/residue: 1.5054 time to fit residues: 4555.5380 Evaluate side-chains 1268 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1228 time to evaluate : 6.765 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 8 residues processed: 40 average time/residue: 1.2569 time to fit residues: 99.3235 ------------------------------------------------------------------------------- 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: 0.9990 chunk 606 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 795 optimal weight: 20.0000 chunk 441 optimal weight: 20.0000 chunk 912 optimal weight: 20.0000 chunk 738 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 545 optimal weight: 0.0270 chunk 959 optimal weight: 1.9990 chunk 269 optimal weight: 10.0000 overall best weight: 4.6050 ------------------------------------------------------------------------------- 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** AC 71 GLN ** AD 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 58 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 159 HIS ** AE 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 130 ASN ** AH 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 79 HIS ** AR 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AR 117 GLN ** AS 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS AS 89 GLN AT 34 ASN AV 57 GLN ** 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** AX 35 ASN Aa 20 ASN ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 7 HIS ** 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 119 GLN ** BH 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 65 ASN BI 73 ASN BI 141 GLN ** BJ 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 51 GLN ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 89 ASN ** BN 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 116 HIS ** BP 49 ASN ** 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 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.9654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.536 163075 Z= 0.319 Angle : 0.979 38.804 242863 Z= 0.481 Chirality : 0.048 2.194 30675 Planarity : 0.008 0.165 13938 Dihedral : 19.905 179.908 61967 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 35.25 Ramachandran Plot: Outliers : 3.29 % Allowed : 20.12 % Favored : 76.59 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.97 % Twisted Proline : 0.60 % Twisted General : 0.53 % 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: -4.82 (0.09), residues: 6565 helix: -1.60 (0.10), residues: 1946 sheet: -2.49 (0.15), residues: 980 loop : -4.57 (0.08), residues: 3639 *********************** 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 1685 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1664 time to evaluate : 6.710 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 outliers start: 21 outliers final: 15 residues processed: 1679 average time/residue: 1.5530 time to fit residues: 4500.9822 Evaluate side-chains 1247 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1232 time to evaluate : 6.835 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 15 average time/residue: 1.2436 time to fit residues: 42.8757 ------------------------------------------------------------------------------- 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: 7.9990 chunk 962 optimal weight: 9.9990 chunk 211 optimal weight: 50.0000 chunk 627 optimal weight: 20.0000 chunk 263 optimal weight: 20.0000 chunk 1070 optimal weight: 7.9990 chunk 888 optimal weight: 20.0000 chunk 495 optimal weight: 0.3980 chunk 88 optimal weight: 20.0000 chunk 353 optimal weight: 30.0000 chunk 561 optimal weight: 0.0270 overall best weight: 5.2844 ------------------------------------------------------------------------------- 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** ** AC 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 87 ASN ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 129 HIS ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 27 ASN ** AG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 89 HIS ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 79 HIS ** AR 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS AS 89 GLN ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AX 50 ASN ** AY 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 41 GLN ** AY 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 60 ASN Aa 47 GLN Ab 43 HIS ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 110 GLN ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 212 GLN BF 224 GLN ** BG 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 62 GLN ** BH 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 123 HIS ** 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 65 ASN ** BI 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 13 ASN ** BJ 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 122 HIS BM 89 ASN ** BN 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 514 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 1.0256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.513 163075 Z= 0.340 Angle : 0.966 37.444 242863 Z= 0.474 Chirality : 0.048 2.293 30675 Planarity : 0.008 0.156 13938 Dihedral : 19.729 179.958 61967 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 37.14 Ramachandran Plot: Outliers : 3.00 % Allowed : 20.76 % Favored : 76.24 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.97 % Twisted Proline : 0.60 % 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: -4.63 (0.09), residues: 6565 helix: -1.41 (0.10), residues: 1959 sheet: -2.43 (0.15), residues: 960 loop : -4.47 (0.08), residues: 3646 *********************** 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 1639 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1622 time to evaluate : 6.834 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 outliers start: 17 outliers final: 14 residues processed: 1633 average time/residue: 1.4708 time to fit residues: 4135.0094 Evaluate side-chains 1247 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1233 time to evaluate : 6.851 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 14 average time/residue: 1.2054 time to fit residues: 39.4623 ------------------------------------------------------------------------------- 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: 30.0000 chunk 120 optimal weight: 20.0000 chunk 609 optimal weight: 20.0000 chunk 781 optimal weight: 30.0000 chunk 605 optimal weight: 8.9990 chunk 900 optimal weight: 6.9990 chunk 597 optimal weight: 7.9990 chunk 1066 optimal weight: 30.0000 chunk 667 optimal weight: 20.0000 chunk 649 optimal weight: 6.9990 chunk 492 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 ** AD 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 66 HIS ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 27 ASN ** AH 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 38 HIS AK 101 HIS ** AM 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 79 HIS ** AR 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS ** AT 102 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 110 ASN ** BH 123 HIS ** 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 65 ASN ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 122 HIS BM 73 GLN BM 89 ASN ** BN 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** BU 16 GLN BU 45 HIS ** BV 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 341 HIS ** CA 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 514 HIS CA 527 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 1.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.505 163075 Z= 0.348 Angle : 0.956 37.646 242863 Z= 0.468 Chirality : 0.048 2.395 30675 Planarity : 0.008 0.155 13938 Dihedral : 19.721 179.931 61967 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 37.76 Ramachandran Plot: Outliers : 2.70 % Allowed : 20.79 % Favored : 76.51 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.99 % Twisted Proline : 0.60 % 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: -4.53 (0.09), residues: 6565 helix: -1.30 (0.11), residues: 1955 sheet: -2.45 (0.15), residues: 982 loop : -4.39 (0.08), residues: 3628 *********************** 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 1601 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1591 time to evaluate : 6.370 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 outliers start: 10 outliers final: 9 residues processed: 1596 average time/residue: 1.4893 time to fit residues: 4109.0392 Evaluate side-chains 1237 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1228 time to evaluate : 6.790 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 9 average time/residue: 1.2405 time to fit residues: 28.2945 ------------------------------------------------------------------------------- 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: 50.0000 chunk 636 optimal weight: 0.9980 chunk 321 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 677 optimal weight: 10.0000 chunk 726 optimal weight: 20.0000 chunk 527 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 837 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 172 HIS ** AD 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 27 ASN ** AG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 38 HIS ** AM 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 57 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AR 66 ASN ** AS 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS ** AU 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 50 GLN ** 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 4 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** ** AZ 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AZ 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 16 HIS ** BF 40 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 116 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** ** BJ 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 122 HIS BM 73 GLN BM 89 ASN ** BN 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 116 HIS ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 71 GLN BU 16 GLN ** BW 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 9 ASN ** CA 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 514 HIS CA 527 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 1.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.498 163075 Z= 0.389 Angle : 1.002 37.613 242863 Z= 0.490 Chirality : 0.048 0.839 30675 Planarity : 0.009 0.182 13938 Dihedral : 19.874 179.818 61967 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 42.26 Ramachandran Plot: Outliers : 2.71 % Allowed : 21.36 % Favored : 75.93 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.99 % Twisted Proline : 0.90 % Twisted General : 0.49 % 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: -4.55 (0.09), residues: 6565 helix: -1.32 (0.11), residues: 1976 sheet: -2.40 (0.16), residues: 925 loop : -4.42 (0.08), residues: 3664 *********************** 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 1607 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1596 time to evaluate : 6.616 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 outliers start: 11 outliers final: 9 residues processed: 1601 average time/residue: 1.4265 time to fit residues: 3908.1105 Evaluate side-chains 1236 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1227 time to evaluate : 6.789 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 9 average time/residue: 1.2081 time to fit residues: 27.5913 ------------------------------------------------------------------------------- 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: 30.0000 chunk 931 optimal weight: 4.9990 chunk 993 optimal weight: 7.9990 chunk 1020 optimal weight: 20.0000 chunk 597 optimal weight: 10.0000 chunk 432 optimal weight: 50.0000 chunk 780 optimal weight: 30.0000 chunk 304 optimal weight: 20.0000 chunk 897 optimal weight: 0.1980 chunk 939 optimal weight: 0.0870 overall best weight: 4.6566 ------------------------------------------------------------------------------- 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** ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 27 ASN ** AG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 132 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** ** AM 128 HIS ** 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** AS 87 HIS ** AU 87 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY 4 GLN ** AY 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AZ 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 40 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 69 HIS ** BG 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 116 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** ** BJ 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 71 GLN BU 16 GLN ** BV 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 14 HIS ** CA 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 292 GLN ** CA 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 514 HIS CA 527 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 1.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.502 163075 Z= 0.339 Angle : 0.950 47.226 242863 Z= 0.465 Chirality : 0.044 0.505 30675 Planarity : 0.008 0.185 13938 Dihedral : 19.659 179.844 61967 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 34.96 Ramachandran Plot: Outliers : 2.44 % Allowed : 20.06 % Favored : 77.50 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.99 % Twisted Proline : 0.60 % 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: -4.37 (0.09), residues: 6565 helix: -1.16 (0.11), residues: 1967 sheet: -2.44 (0.16), residues: 968 loop : -4.28 (0.09), residues: 3630 *********************** 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 1584 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1573 time to evaluate : 6.778 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 outliers start: 11 outliers final: 9 residues processed: 1579 average time/residue: 1.4021 time to fit residues: 3809.7881 Evaluate side-chains 1245 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1236 time to evaluate : 6.826 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 9 average time/residue: 1.2022 time to fit residues: 27.5273 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1050 optimal weight: 9.9990 chunk 641 optimal weight: 5.9990 chunk 498 optimal weight: 8.9990 chunk 730 optimal weight: 20.0000 chunk 1101 optimal weight: 40.0000 chunk 1014 optimal weight: 5.9990 chunk 877 optimal weight: 20.0000 chunk 91 optimal weight: 40.0000 chunk 677 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 44 ASN ** AD 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 121 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS AS 89 GLN ** AU 87 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 38 GLN ** 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 60 ASN ** AZ 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 69 HIS ** BG 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 110 ASN ** BG 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 116 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 65 ASN ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 73 GLN BM 89 ASN ** BN 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 116 HIS ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 50 HIS BU 16 GLN ** BV 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 14 HIS ** BX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 514 HIS CA 527 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 1.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.520 163075 Z= 0.393 Angle : 0.973 37.171 242863 Z= 0.477 Chirality : 0.046 0.521 30675 Planarity : 0.008 0.155 13938 Dihedral : 19.736 179.707 61967 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 40.29 Ramachandran Plot: Outliers : 2.42 % Allowed : 21.22 % Favored : 76.36 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.99 % 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: -4.39 (0.09), residues: 6565 helix: -1.17 (0.11), residues: 1967 sheet: -2.43 (0.16), residues: 979 loop : -4.30 (0.08), residues: 3619 ********************** 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 1548 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1538 time to evaluate : 6.797 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 outliers start: 10 outliers final: 9 residues processed: 1543 average time/residue: 1.4499 time to fit residues: 3869.6357 Evaluate side-chains 1214 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1205 time to evaluate : 6.752 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 9 average time/residue: 1.2069 time to fit residues: 27.5192 ------------------------------------------------------------------------------- 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: 10.0000 chunk 696 optimal weight: 20.0000 chunk 934 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 809 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 878 optimal weight: 9.9990 chunk 367 optimal weight: 0.0970 chunk 902 optimal weight: 8.9990 chunk 111 optimal weight: 40.0000 overall best weight: 7.6186 ------------------------------------------------------------------------------- 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 44 ASN AD 96 HIS ** AD 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 85 ASN ** AF 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS AS 89 GLN ** AU 87 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 38 GLN ** 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 60 ASN ** AZ 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 19 HIS ** BF 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 110 ASN ** BG 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 116 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 65 ASN ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 122 HIS BL 82 HIS ** BM 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 73 GLN BM 89 ASN ** BN 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 50 HIS ** BS 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 16 GLN ** BV 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 14 HIS BX 73 HIS ** CA 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 527 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.084130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.067365 restraints weight = 705086.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.069461 restraints weight = 280587.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.070654 restraints weight = 147805.744| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 1.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.503 163075 Z= 0.390 Angle : 0.980 36.973 242863 Z= 0.482 Chirality : 0.046 0.504 30675 Planarity : 0.008 0.157 13938 Dihedral : 19.819 179.989 61967 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 40.39 Ramachandran Plot: Outliers : 2.36 % Allowed : 20.99 % Favored : 76.65 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.99 % Twisted Proline : 0.90 % Twisted General : 0.51 % 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: -4.44 (0.09), residues: 6565 helix: -1.29 (0.11), residues: 1999 sheet: -2.34 (0.16), residues: 943 loop : -4.33 (0.08), residues: 3623 =============================================================================== Job complete usr+sys time: 59403.56 seconds wall clock time: 1016 minutes 58.00 seconds (61018.00 seconds total)