Starting phenix.real_space_refine on Tue Mar 19 21:00:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6x_10709/03_2024/6y6x_10709_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6x_10709/03_2024/6y6x_10709.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6x_10709/03_2024/6y6x_10709_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6x_10709/03_2024/6y6x_10709_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6x_10709/03_2024/6y6x_10709_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6x_10709/03_2024/6y6x_10709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6x_10709/03_2024/6y6x_10709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6x_10709/03_2024/6y6x_10709_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6x_10709/03_2024/6y6x_10709_trim_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 4047 5.49 5 Mg 229 5.21 5 S 246 5.16 5 C 72875 2.51 5 N 26370 2.21 5 O 37197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "LA ARG 30": "NH1" <-> "NH2" Residue "LA GLU 36": "OE1" <-> "OE2" Residue "LA GLU 80": "OE1" <-> "OE2" Residue "LA ARG 128": "NH1" <-> "NH2" Residue "LA ARG 198": "NH1" <-> "NH2" Residue "LA ARG 245": "NH1" <-> "NH2" Residue "LB ARG 10": "NH1" <-> "NH2" Residue "LB GLU 74": "OE1" <-> "OE2" Residue "LB ARG 97": "NH1" <-> "NH2" Residue "LB GLU 140": "OE1" <-> "OE2" Residue "LB ARG 198": "NH1" <-> "NH2" Residue "LB GLU 199": "OE1" <-> "OE2" Residue "LB ARG 268": "NH1" <-> "NH2" Residue "LB PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 361": "OE1" <-> "OE2" Residue "LB ARG 378": "NH1" <-> "NH2" Residue "LC GLU 16": "OE1" <-> "OE2" Residue "LC ARG 49": "NH1" <-> "NH2" Residue "LC GLU 56": "OE1" <-> "OE2" Residue "LC GLU 65": "OE1" <-> "OE2" Residue "LC ARG 78": "NH1" <-> "NH2" Residue "LC ARG 109": "NH1" <-> "NH2" Residue "LC ARG 110": "NH1" <-> "NH2" Residue "LC ARG 204": "NH1" <-> "NH2" Residue "LC ARG 205": "NH1" <-> "NH2" Residue "LC GLU 254": "OE1" <-> "OE2" Residue "LC GLU 262": "OE1" <-> "OE2" Residue "LC ARG 300": "NH1" <-> "NH2" Residue "LC ARG 311": "NH1" <-> "NH2" Residue "LC ARG 323": "NH1" <-> "NH2" Residue "LC ARG 337": "NH1" <-> "NH2" Residue "LD ARG 23": "NH1" <-> "NH2" Residue "LD ARG 24": "NH1" <-> "NH2" Residue "LD ARG 33": "NH1" <-> "NH2" Residue "LD ARG 108": "NH1" <-> "NH2" Residue "LD GLU 120": "OE1" <-> "OE2" Residue "LD GLU 124": "OE1" <-> "OE2" Residue "LD GLU 133": "OE1" <-> "OE2" Residue "LD ARG 179": "NH1" <-> "NH2" Residue "LD GLU 189": "OE1" <-> "OE2" Residue "LD GLU 193": "OE1" <-> "OE2" Residue "LD ARG 209": "NH1" <-> "NH2" Residue "LD GLU 213": "OE1" <-> "OE2" Residue "LD GLU 216": "OE1" <-> "OE2" Residue "LD GLU 254": "OE1" <-> "OE2" Residue "LD GLU 292": "OE1" <-> "OE2" Residue "LE GLU 119": "OE1" <-> "OE2" Residue "LE ARG 161": "NH1" <-> "NH2" Residue "LE ARG 188": "NH1" <-> "NH2" Residue "LE ARG 223": "NH1" <-> "NH2" Residue "LE GLU 229": "OE1" <-> "OE2" Residue "LE GLU 236": "OE1" <-> "OE2" Residue "LF GLU 27": "OE1" <-> "OE2" Residue "LF ARG 43": "NH1" <-> "NH2" Residue "LF ARG 46": "NH1" <-> "NH2" Residue "LF ARG 94": "NH1" <-> "NH2" Residue "LF ARG 134": "NH1" <-> "NH2" Residue "LF GLU 152": "OE1" <-> "OE2" Residue "LF ARG 157": "NH1" <-> "NH2" Residue "LF GLU 237": "OE1" <-> "OE2" Residue "LF ARG 245": "NH1" <-> "NH2" Residue "LG ARG 35": "NH1" <-> "NH2" Residue "LG ARG 59": "NH1" <-> "NH2" Residue "LG ARG 89": "NH1" <-> "NH2" Residue "LG ARG 189": "NH1" <-> "NH2" Residue "LG GLU 220": "OE1" <-> "OE2" Residue "LG ARG 234": "NH1" <-> "NH2" Residue "LH GLU 14": "OE1" <-> "OE2" Residue "LH ARG 23": "NH1" <-> "NH2" Residue "LH GLU 66": "OE1" <-> "OE2" Residue "LH ARG 89": "NH1" <-> "NH2" Residue "LH ARG 93": "NH1" <-> "NH2" Residue "LH GLU 143": "OE1" <-> "OE2" Residue "LI ARG 4": "NH1" <-> "NH2" Residue "LI ARG 7": "NH1" <-> "NH2" Residue "LI ARG 24": "NH1" <-> "NH2" Residue "LI ARG 38": "NH1" <-> "NH2" Residue "LI GLU 56": "OE1" <-> "OE2" Residue "LI ARG 69": "NH1" <-> "NH2" Residue "LI ARG 98": "NH1" <-> "NH2" Residue "LI ARG 116": "NH1" <-> "NH2" Residue "LI ARG 153": "NH1" <-> "NH2" Residue "LI ARG 162": "NH1" <-> "NH2" Residue "LI GLU 180": "OE1" <-> "OE2" Residue "LI ARG 210": "NH1" <-> "NH2" Residue "LJ ARG 35": "NH1" <-> "NH2" Residue "LJ GLU 41": "OE1" <-> "OE2" Residue "LJ ARG 63": "NH1" <-> "NH2" Residue "LJ ARG 64": "NH1" <-> "NH2" Residue "LJ GLU 80": "OE1" <-> "OE2" Residue "LJ GLU 81": "OE1" <-> "OE2" Residue "LJ GLU 84": "OE1" <-> "OE2" Residue "LJ GLU 91": "OE1" <-> "OE2" Residue "LJ GLU 111": "OE1" <-> "OE2" Residue "LL ARG 21": "NH1" <-> "NH2" Residue "LL ARG 31": "NH1" <-> "NH2" Residue "LL ARG 36": "NH1" <-> "NH2" Residue "LL ARG 65": "NH1" <-> "NH2" Residue "LL ARG 102": "NH1" <-> "NH2" Residue "LL ARG 116": "NH1" <-> "NH2" Residue "LL ARG 158": "NH1" <-> "NH2" Residue "LL GLU 171": "OE1" <-> "OE2" Residue "LL GLU 172": "OE1" <-> "OE2" Residue "LL GLU 173": "OE1" <-> "OE2" Residue "LL GLU 204": "OE1" <-> "OE2" Residue "LM GLU 96": "OE1" <-> "OE2" Residue "LM ARG 98": "NH1" <-> "NH2" Residue "LM ARG 109": "NH1" <-> "NH2" Residue "LM ARG 119": "NH1" <-> "NH2" Residue "LM ARG 121": "NH1" <-> "NH2" Residue "LN ARG 20": "NH1" <-> "NH2" Residue "LN ARG 50": "NH1" <-> "NH2" Residue "LN ARG 65": "NH1" <-> "NH2" Residue "LN ARG 96": "NH1" <-> "NH2" Residue "LN ARG 108": "NH1" <-> "NH2" Residue "LN ARG 169": "NH1" <-> "NH2" Residue "LN ARG 189": "NH1" <-> "NH2" Residue "LN ARG 194": "NH1" <-> "NH2" Residue "LO ARG 37": "NH1" <-> "NH2" Residue "LO ARG 49": "NH1" <-> "NH2" Residue "LO ARG 78": "NH1" <-> "NH2" Residue "LO ARG 128": "NH1" <-> "NH2" Residue "LO ARG 140": "NH1" <-> "NH2" Residue "LO GLU 158": "OE1" <-> "OE2" Residue "LO GLU 162": "OE1" <-> "OE2" Residue "LP ARG 3": "NH1" <-> "NH2" Residue "LP ARG 30": "NH1" <-> "NH2" Residue "LP ARG 61": "NH1" <-> "NH2" Residue "LP ARG 62": "NH1" <-> "NH2" Residue "LQ ASP 4": "OD1" <-> "OD2" Residue "LQ GLU 17": "OE1" <-> "OE2" Residue "LQ ARG 37": "NH1" <-> "NH2" Residue "LQ ARG 55": "NH1" <-> "NH2" Residue "LQ ARG 91": "NH1" <-> "NH2" Residue "LQ GLU 94": "OE1" <-> "OE2" Residue "LQ ARG 108": "NH1" <-> "NH2" Residue "LQ GLU 147": "OE1" <-> "OE2" Residue "LQ GLU 175": "OE1" <-> "OE2" Residue "LQ ARG 180": "NH1" <-> "NH2" Residue "LR GLU 31": "OE1" <-> "OE2" Residue "LR ARG 38": "NH1" <-> "NH2" Residue "LR ARG 42": "NH1" <-> "NH2" Residue "LR ARG 52": "NH1" <-> "NH2" Residue "LR ARG 74": "NH1" <-> "NH2" Residue "LR GLU 91": "OE1" <-> "OE2" Residue "LR ARG 117": "NH1" <-> "NH2" Residue "LS ARG 31": "NH1" <-> "NH2" Residue "LS ARG 43": "NH1" <-> "NH2" Residue "LS ARG 83": "NH1" <-> "NH2" Residue "LS ARG 111": "NH1" <-> "NH2" Residue "LS ARG 118": "NH1" <-> "NH2" Residue "LS GLU 130": "OE1" <-> "OE2" Residue "LS GLU 131": "OE1" <-> "OE2" Residue "LS ARG 139": "NH1" <-> "NH2" Residue "LT ARG 8": "NH1" <-> "NH2" Residue "LT ARG 17": "NH1" <-> "NH2" Residue "LT GLU 118": "OE1" <-> "OE2" Residue "LT ARG 130": "NH1" <-> "NH2" Residue "LT ARG 136": "NH1" <-> "NH2" Residue "LT GLU 149": "OE1" <-> "OE2" Residue "LU GLU 40": "OE1" <-> "OE2" Residue "LV ARG 48": "NH1" <-> "NH2" Residue "LV ARG 51": "NH1" <-> "NH2" Residue "LV ARG 83": "NH1" <-> "NH2" Residue "LV ARG 89": "NH1" <-> "NH2" Residue "LV ARG 131": "NH1" <-> "NH2" Residue "LW ARG 19": "NH1" <-> "NH2" Residue "LW GLU 37": "OE1" <-> "OE2" Residue "LW TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ARG 53": "NH1" <-> "NH2" Residue "LX GLU 84": "OE1" <-> "OE2" Residue "LX ASP 118": "OD1" <-> "OD2" Residue "LX ARG 139": "NH1" <-> "NH2" Residue "LY ARG 27": "NH1" <-> "NH2" Residue "LY GLU 37": "OE1" <-> "OE2" Residue "LY GLU 54": "OE1" <-> "OE2" Residue "LY GLU 83": "OE1" <-> "OE2" Residue "LY ARG 87": "NH1" <-> "NH2" Residue "LY GLU 88": "OE1" <-> "OE2" Residue "LY GLU 120": "OE1" <-> "OE2" Residue "LY GLU 131": "OE1" <-> "OE2" Residue "LZ ARG 65": "NH1" <-> "NH2" Residue "LZ ARG 84": "NH1" <-> "NH2" Residue "LZ GLU 120": "OE1" <-> "OE2" Residue "La ARG 21": "NH1" <-> "NH2" Residue "La ARG 65": "NH1" <-> "NH2" Residue "La ARG 105": "NH1" <-> "NH2" Residue "La ARG 131": "NH1" <-> "NH2" Residue "Lb ARG 14": "NH1" <-> "NH2" Residue "Lb ARG 18": "NH1" <-> "NH2" Residue "Lb ARG 28": "NH1" <-> "NH2" Residue "Lb ARG 91": "NH1" <-> "NH2" Residue "Lc GLU 12": "OE1" <-> "OE2" Residue "Lc ARG 39": "NH1" <-> "NH2" Residue "Lc GLU 61": "OE1" <-> "OE2" Residue "Ld GLU 24": "OE1" <-> "OE2" Residue "Ld ARG 90": "NH1" <-> "NH2" Residue "Ld GLU 96": "OE1" <-> "OE2" Residue "Ld TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le ARG 36": "NH1" <-> "NH2" Residue "Le ARG 39": "NH1" <-> "NH2" Residue "Le ARG 47": "NH1" <-> "NH2" Residue "Le ARG 128": "NH1" <-> "NH2" Residue "Lf GLU 31": "OE1" <-> "OE2" Residue "Lf ARG 36": "NH1" <-> "NH2" Residue "Lf GLU 38": "OE1" <-> "OE2" Residue "Lf GLU 40": "OE1" <-> "OE2" Residue "Lf ARG 89": "NH1" <-> "NH2" Residue "Lg ARG 60": "NH1" <-> "NH2" Residue "Lg GLU 98": "OE1" <-> "OE2" Residue "Lh ARG 7": "NH1" <-> "NH2" Residue "Lh GLU 15": "OE1" <-> "OE2" Residue "Lh GLU 16": "OE1" <-> "OE2" Residue "Lh GLU 27": "OE1" <-> "OE2" Residue "Lh ARG 56": "NH1" <-> "NH2" Residue "Lh ARG 94": "NH1" <-> "NH2" Residue "Lh GLU 100": "OE1" <-> "OE2" Residue "Li ARG 25": "NH1" <-> "NH2" Residue "Li ARG 45": "NH1" <-> "NH2" Residue "Li ARG 68": "NH1" <-> "NH2" Residue "Li ARG 76": "NH1" <-> "NH2" Residue "Li GLU 89": "OE1" <-> "OE2" Residue "Lj ARG 45": "NH1" <-> "NH2" Residue "Lj ARG 55": "NH1" <-> "NH2" Residue "Lj ARG 56": "NH1" <-> "NH2" Residue "Lj ARG 72": "NH1" <-> "NH2" Residue "Lj ARG 79": "NH1" <-> "NH2" Residue "Lk ARG 3": "NH1" <-> "NH2" Residue "Lk GLU 6": "OE1" <-> "OE2" Residue "Lk ARG 40": "NH1" <-> "NH2" Residue "Ll ARG 28": "NH1" <-> "NH2" Residue "Ll ARG 42": "NH1" <-> "NH2" Residue "Ll ARG 45": "NH1" <-> "NH2" Residue "Lm ARG 97": "NH1" <-> "NH2" Residue "Lm ARG 106": "NH1" <-> "NH2" Residue "Lm ARG 111": "NH1" <-> "NH2" Residue "Ln ARG 2": "NH1" <-> "NH2" Residue "Ln ARG 23": "NH1" <-> "NH2" Residue "Lo ARG 40": "NH1" <-> "NH2" Residue "Lo ARG 43": "NH1" <-> "NH2" Residue "Lo ARG 78": "NH1" <-> "NH2" Residue "Lp ARG 17": "NH1" <-> "NH2" Residue "Lp ARG 49": "NH1" <-> "NH2" Residue "Lp ARG 84": "NH1" <-> "NH2" Residue "Lp GLU 88": "OE1" <-> "OE2" Residue "Lr ARG 71": "NH1" <-> "NH2" Residue "Lr ARG 112": "NH1" <-> "NH2" Residue "Lr ARG 113": "NH1" <-> "NH2" Residue "Lz GLU 16": "OE1" <-> "OE2" Residue "Lz GLU 76": "OE1" <-> "OE2" Residue "Lz GLU 88": "OE1" <-> "OE2" Residue "Lz GLU 114": "OE1" <-> "OE2" Residue "Lz GLU 142": "OE1" <-> "OE2" Residue "Lz GLU 150": "OE1" <-> "OE2" Residue "Lz ARG 202": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 140969 Number of models: 1 Model: "" Number of chains: 60 Chain: "L5" Number of atoms: 80136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3773, 80136 Classifications: {'DNA': 52, 'RNA': 3721} Modifications used: {'5*END': 1, 'rna2p_pur': 364, 'rna2p_pyr': 238, 'rna3p_pur': 1669, 'rna3p_pyr': 1446} Link IDs: {'rna2p': 601, 'rna3p': 3171} Chain breaks: 10 Unresolved non-hydrogen bonds: 831 Unresolved non-hydrogen angles: 1357 Unresolved non-hydrogen dihedrals: 605 Unresolved non-hydrogen chiralities: 172 Planarities with less than four sites: {' G:plan2': 24, ' A:plan': 1, ' C:plan': 27, ' U:plan': 4, ' G:plan': 24, ' C:plan2': 27, ' A:plan2': 1} Unresolved non-hydrogen planarities: 682 Chain: "L7" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2561 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 54} Link IDs: {'rna2p': 11, 'rna3p': 108} Chain: "L8" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3314 Classifications: {'RNA': 156} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 13, 'rna3p_pur': 62, 'rna3p_pyr': 67} Link IDs: {'rna2p': 27, 'rna3p': 128} Chain: "LA" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1898 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 14, 'TRANS': 233} Chain: "LB" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3202 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 15, 'TRANS': 381} Chain: "LC" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2927 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 348} Chain: "LD" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2382 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LE" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1904 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 14, 'TRANS': 218} Chain breaks: 1 Chain: "LF" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "LG" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1927 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 225} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "LH" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "LI" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1634 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "LJ" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1410 Classifications: {'peptide': 176} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 169} Chain: "LL" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "LM" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1138 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "LN" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "LO" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1650 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "LP" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "LQ" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 175} Chain: "LR" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1434 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 183} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "LS" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1453 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 163} Chain: "LT" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "LU" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 809 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "LV" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "LW" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 833 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 96 Chain: "LX" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 985 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 110} Chain: "LY" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LZ" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "La" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 139} Chain: "Lb" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Lc" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 764 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "Ld" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Le" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "Lf" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "Lg" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Lh" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Li" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Lj" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "Lk" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "Ll" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lm" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "Ln" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 230 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "Lo" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 862 Classifications: {'peptide': 105} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "Lp" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "Lr" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "Lz" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1738 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L5" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 249 Unusual residues: {' MG': 214, 'OCW': 1} Classifications: {'undetermined': 215} Link IDs: {None: 214} Chain: "L7" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L8" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "LA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Le" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Lg" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Lj" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Lm" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lo" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0QCP SG CYSLj 19 70.712 169.930 171.925 1.00 20.04 S ATOM A0QDH SG CYSLj 22 69.393 171.100 167.566 1.00 19.78 S ATOM A0QG0 SG CYSLj 34 72.965 170.496 169.053 1.00 20.98 S ATOM A0QGJ SG CYSLj 37 70.970 173.472 169.793 1.00 18.92 S ATOM A0RP1 SG CYSLm 96 144.869 131.256 92.632 1.00 22.70 S ATOM A0RPR SG CYSLm 99 142.017 129.103 93.397 1.00 23.94 S ATOM A0RS9 SG CYSLm 110 142.843 129.153 89.787 1.00 21.02 S ATOM A0RTH SG CYSLm 115 141.218 132.243 90.810 1.00 23.50 S ATOM A0S5D SG CYSLo 12 130.084 233.901 134.322 1.00 30.86 S ATOM A0SJ2 SG CYSLo 72 133.191 235.010 136.425 1.00 44.16 S ATOM A0SK3 SG CYSLo 77 130.207 238.598 136.708 1.00 71.13 S ATOM A0SZ4 SG CYSLp 39 112.355 147.852 218.011 1.00 23.20 S ATOM A0SZR SG CYSLp 42 111.355 144.420 219.975 1.00 26.50 S ATOM A0T35 SG CYSLp 57 110.060 145.304 216.509 1.00 24.70 S ATOM A0T3L SG CYSLp 60 108.812 147.800 218.908 1.00 30.53 S Time building chain proxies: 52.76, per 1000 atoms: 0.37 Number of scatterers: 140969 At special positions: 0 Unit cell: (216.8, 308.94, 291.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 246 16.00 P 4047 15.00 Mg 229 11.99 O 37197 8.00 N 26370 7.00 C 72875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.09 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLj 102 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 34 " pdb=" ZNLm 201 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 115 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 96 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 99 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 110 " pdb=" ZNLo 201 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 12 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 72 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 77 " pdb=" ZNLp 101 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 39 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 57 " Number of angles added : 18 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12676 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 228 helices and 67 sheets defined 41.5% alpha, 14.1% beta 1277 base pairs and 2073 stacking pairs defined. Time for finding SS restraints: 70.73 Creating SS restraints... Processing helix chain 'LA' and resid 5 through 13 removed outlier: 5.845A pdb=" N LYSLA 10 " --> pdb=" O ARGLA 6 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALALA 12 " --> pdb=" O GLNLA 8 " (cutoff:3.500A) Processing helix chain 'LA' and resid 33 through 38 Processing helix chain 'LA' and resid 103 through 108 Proline residue: LA 108 - end of helix Processing helix chain 'LA' and resid 181 through 193 Processing helix chain 'LA' and resid 200 through 205 removed outlier: 4.969A pdb=" N ASNLA 205 " --> pdb=" O GLYLA 201 " (cutoff:3.500A) Processing helix chain 'LA' and resid 173 through 178 Proline residue: LA 178 - end of helix Processing helix chain 'LB' and resid 111 through 120 removed outlier: 5.014A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 140 removed outlier: 5.256A pdb=" N GLULB 140 " --> pdb=" O LYSLB 136 " (cutoff:3.500A) Processing helix chain 'LB' and resid 141 through 157 Processing helix chain 'LB' and resid 167 through 172 removed outlier: 4.658A pdb=" N LEULB 171 " --> pdb=" O GLNLB 167 " (cutoff:3.500A) Proline residue: LB 172 - end of helix No H-bonds generated for 'chain 'LB' and resid 167 through 172' Processing helix chain 'LB' and resid 189 through 201 Processing helix chain 'LB' and resid 206 through 211 Processing helix chain 'LB' and resid 230 through 235 Processing helix chain 'LB' and resid 299 through 304 removed outlier: 4.776A pdb=" N ALALB 303 " --> pdb=" O ILELB 299 " (cutoff:3.500A) Processing helix chain 'LB' and resid 356 through 361 removed outlier: 4.924A pdb=" N GLULB 361 " --> pdb=" O ARGLB 357 " (cutoff:3.500A) Processing helix chain 'LB' and resid 381 through 390 Processing helix chain 'LB' and resid 392 through 398 Processing helix chain 'LC' and resid 25 through 30 Processing helix chain 'LC' and resid 33 through 49 removed outlier: 4.318A pdb=" N ASNLC 48 " --> pdb=" O LEULC 44 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARGLC 49 " --> pdb=" O ARGLC 45 " (cutoff:3.500A) Processing helix chain 'LC' and resid 116 through 134 Proline residue: LC 134 - end of helix Processing helix chain 'LC' and resid 135 through 141 Processing helix chain 'LC' and resid 155 through 161 removed outlier: 4.608A pdb=" N GLULC 159 " --> pdb=" O GLULC 155 " (cutoff:3.500A) Processing helix chain 'LC' and resid 163 through 175 Processing helix chain 'LC' and resid 176 through 187 Processing helix chain 'LC' and resid 193 through 198 Processing helix chain 'LC' and resid 216 through 222 Processing helix chain 'LC' and resid 236 through 242 Proline residue: LC 242 - end of helix Processing helix chain 'LC' and resid 253 through 264 removed outlier: 4.569A pdb=" N ASPLC 261 " --> pdb=" O PHELC 257 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLULC 262 " --> pdb=" O ARGLC 258 " (cutoff:3.500A) Processing helix chain 'LC' and resid 288 through 295 Processing helix chain 'LC' and resid 296 through 303 removed outlier: 5.757A pdb=" N ARGLC 303 " --> pdb=" O GLNLC 299 " (cutoff:3.500A) Processing helix chain 'LC' and resid 321 through 329 Processing helix chain 'LC' and resid 330 through 366 removed outlier: 4.657A pdb=" N THRLC 334 " --> pdb=" O PROLC 330 " (cutoff:3.500A) Processing helix chain 'LD' and resid 9 through 16 Processing helix chain 'LD' and resid 20 through 26 Processing helix chain 'LD' and resid 29 through 37 Processing helix chain 'LD' and resid 79 through 84 Proline residue: LD 84 - end of helix Processing helix chain 'LD' and resid 94 through 114 Processing helix chain 'LD' and resid 115 through 120 removed outlier: 4.436A pdb=" N TYRLD 119 " --> pdb=" O METLD 115 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLULD 120 " --> pdb=" O ASPLD 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'LD' and resid 115 through 120' Processing helix chain 'LD' and resid 157 through 170 Processing helix chain 'LD' and resid 191 through 201 removed outlier: 6.128A pdb=" N HISLD 195 " --> pdb=" O ASNLD 191 " (cutoff:3.500A) Processing helix chain 'LD' and resid 202 through 215 Processing helix chain 'LD' and resid 216 through 224 Processing helix chain 'LD' and resid 225 through 230 removed outlier: 5.020A pdb=" N ASNLD 229 " --> pdb=" O GLNLD 225 " (cutoff:3.500A) Processing helix chain 'LD' and resid 235 through 250 removed outlier: 3.863A pdb=" N METLD 239 " --> pdb=" O METLD 235 " (cutoff:3.500A) Processing helix chain 'LD' and resid 272 through 294 Processing helix chain 'LE' and resid 58 through 67 Processing helix chain 'LE' and resid 190 through 195 removed outlier: 5.504A pdb=" N ILELE 195 " --> pdb=" O GLNLE 191 " (cutoff:3.500A) Processing helix chain 'LE' and resid 213 through 218 Processing helix chain 'LE' and resid 243 through 264 Proline residue: LE 259 - end of helix removed outlier: 4.274A pdb=" N ILELE 264 " --> pdb=" O LYSLE 260 " (cutoff:3.500A) Processing helix chain 'LE' and resid 266 through 274 removed outlier: 5.035A pdb=" N VALLE 274 " --> pdb=" O TYRLE 270 " (cutoff:3.500A) Processing helix chain 'LF' and resid 24 through 79 removed outlier: 4.540A pdb=" N LYSLF 29 " --> pdb=" O PHELF 25 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 113 Processing helix chain 'LF' and resid 126 through 137 Processing helix chain 'LF' and resid 146 through 156 Processing helix chain 'LF' and resid 171 through 179 Processing helix chain 'LF' and resid 186 through 197 Processing helix chain 'LF' and resid 200 through 209 removed outlier: 5.143A pdb=" N TRPLF 209 " --> pdb=" O ASNLF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 238 through 248 removed outlier: 4.416A pdb=" N ARGLF 242 " --> pdb=" O ASPLF 238 " (cutoff:3.500A) Processing helix chain 'LG' and resid 58 through 74 Processing helix chain 'LG' and resid 77 through 86 removed outlier: 4.786A pdb=" N PHELG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALALG 86 " --> pdb=" O GLNLG 82 " (cutoff:3.500A) Processing helix chain 'LG' and resid 88 through 103 removed outlier: 3.627A pdb=" N TYRLG 102 " --> pdb=" O LEULG 98 " (cutoff:3.500A) Processing helix chain 'LG' and resid 106 through 124 Processing helix chain 'LG' and resid 139 through 150 Processing helix chain 'LG' and resid 164 through 178 removed outlier: 5.598A pdb=" N VALLG 168 " --> pdb=" O ILELG 164 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N PHELG 169 " --> pdb=" O GLULG 165 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEULG 170 " --> pdb=" O LEULG 166 " (cutoff:3.500A) Proline residue: LG 171 - end of helix Processing helix chain 'LG' and resid 186 through 195 Processing helix chain 'LG' and resid 208 through 226 removed outlier: 4.586A pdb=" N GLYLG 213 " --> pdb=" O SERLG 209 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALALG 214 " --> pdb=" O GLULG 210 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLULG 220 " --> pdb=" O ALALG 216 " (cutoff:3.500A) Processing helix chain 'LG' and resid 229 through 236 Processing helix chain 'LG' and resid 243 through 266 removed outlier: 5.053A pdb=" N GLULG 260 " --> pdb=" O ALALG 256 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THRLG 263 " --> pdb=" O LYSLG 259 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLYLG 266 " --> pdb=" O ALALG 262 " (cutoff:3.500A) Processing helix chain 'LH' and resid 63 through 86 removed outlier: 4.523A pdb=" N THRLH 69 " --> pdb=" O LYSLH 65 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VALLH 70 " --> pdb=" O GLULH 66 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARGLH 71 " --> pdb=" O LEULH 67 " (cutoff:3.500A) Processing helix chain 'LH' and resid 150 through 166 removed outlier: 4.348A pdb=" N THRLH 166 " --> pdb=" O GLNLH 162 " (cutoff:3.500A) Processing helix chain 'LH' and resid 171 through 176 removed outlier: 5.559A pdb=" N LEULH 176 " --> pdb=" O ILELH 172 " (cutoff:3.500A) Processing helix chain 'LI' and resid 5 through 10 removed outlier: 4.407A pdb=" N TYRLI 9 " --> pdb=" O PROLI 5 " (cutoff:3.500A) Processing helix chain 'LI' and resid 42 through 47 removed outlier: 6.543A pdb=" N PHELI 46 " --> pdb=" O LYSLI 42 " (cutoff:3.500A) Proline residue: LI 47 - end of helix No H-bonds generated for 'chain 'LI' and resid 42 through 47' Processing helix chain 'LI' and resid 61 through 80 Processing helix chain 'LI' and resid 144 through 159 removed outlier: 4.737A pdb=" N LYSLI 158 " --> pdb=" O ARGLI 154 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHELI 159 " --> pdb=" O ALALI 155 " (cutoff:3.500A) Processing helix chain 'LI' and resid 177 through 188 removed outlier: 4.616A pdb=" N GLULI 182 " --> pdb=" O ALALI 178 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASPLI 183 " --> pdb=" O ASPLI 179 " (cutoff:3.500A) Processing helix chain 'LI' and resid 205 through 213 Processing helix chain 'LJ' and resid 3 through 8 removed outlier: 5.041A pdb=" N LYSLJ 8 " --> pdb=" O ASPLJ 4 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 30 through 44 removed outlier: 3.701A pdb=" N LEULJ 40 " --> pdb=" O ALALJ 36 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 76 through 91 Processing helix chain 'LJ' and resid 139 through 144 removed outlier: 4.717A pdb=" N ASPLJ 143 " --> pdb=" O PHELJ 139 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 158 through 171 Processing helix chain 'LL' and resid 17 through 22 removed outlier: 4.385A pdb=" N ARGLL 21 " --> pdb=" O ASPLL 17 " (cutoff:3.500A) Processing helix chain 'LL' and resid 27 through 47 Processing helix chain 'LL' and resid 77 through 85 Processing helix chain 'LL' and resid 87 through 95 removed outlier: 4.328A pdb=" N ARGLL 92 " --> pdb=" O LYSLL 88 " (cutoff:3.500A) Processing helix chain 'LL' and resid 106 through 124 Processing helix chain 'LL' and resid 139 through 146 Processing helix chain 'LL' and resid 170 through 176 Processing helix chain 'LL' and resid 177 through 192 Processing helix chain 'LL' and resid 193 through 209 Processing helix chain 'LM' and resid 51 through 56 removed outlier: 5.170A pdb=" N GLNLM 56 " --> pdb=" O PHELM 52 " (cutoff:3.500A) Processing helix chain 'LM' and resid 69 through 81 removed outlier: 5.079A pdb=" N ALALM 80 " --> pdb=" O ALALM 76 " (cutoff:3.500A) Processing helix chain 'LM' and resid 82 through 89 removed outlier: 4.759A pdb=" N ALALM 87 " --> pdb=" O ASNLM 83 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALALM 88 " --> pdb=" O THRLM 84 " (cutoff:3.500A) Processing helix chain 'LM' and resid 90 through 104 Processing helix chain 'LM' and resid 106 through 136 removed outlier: 4.457A pdb=" N LEULM 136 " --> pdb=" O LYSLM 132 " (cutoff:3.500A) Processing helix chain 'LN' and resid 2 through 14 removed outlier: 4.395A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 4.960A pdb=" N SERLN 34 " --> pdb=" O TYRLN 30 " (cutoff:3.500A) Processing helix chain 'LN' and resid 44 through 52 Processing helix chain 'LN' and resid 83 through 88 removed outlier: 4.647A pdb=" N GLYLN 88 " --> pdb=" O PROLN 84 " (cutoff:3.500A) Processing helix chain 'LN' and resid 97 through 111 Processing helix chain 'LN' and resid 139 through 145 removed outlier: 4.904A pdb=" N ASNLN 145 " --> pdb=" O ALALN 141 " (cutoff:3.500A) Processing helix chain 'LN' and resid 148 through 154 removed outlier: 4.335A pdb=" N THRLN 152 " --> pdb=" O THRLN 148 " (cutoff:3.500A) Proline residue: LN 154 - end of helix Processing helix chain 'LN' and resid 158 through 163 Processing helix chain 'LN' and resid 165 through 173 Processing helix chain 'LN' and resid 187 through 197 Processing helix chain 'LO' and resid 15 through 30 Processing helix chain 'LO' and resid 46 through 61 removed outlier: 5.398A pdb=" N ARGLO 61 " --> pdb=" O PHELO 57 " (cutoff:3.500A) Processing helix chain 'LO' and resid 65 through 70 Proline residue: LO 70 - end of helix Processing helix chain 'LO' and resid 75 through 89 Proline residue: LO 89 - end of helix Processing helix chain 'LO' and resid 92 through 103 removed outlier: 5.424A pdb=" N LYSLO 103 " --> pdb=" O LEULO 99 " (cutoff:3.500A) Processing helix chain 'LO' and resid 124 through 129 Processing helix chain 'LO' and resid 137 through 146 Processing helix chain 'LO' and resid 151 through 190 removed outlier: 6.223A pdb=" N LYSLO 187 " --> pdb=" O LYSLO 183 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYSLO 188 " --> pdb=" O ASNLO 184 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILELO 189 " --> pdb=" O VALLO 185 " (cutoff:3.500A) Processing helix chain 'LO' and resid 191 through 200 removed outlier: 4.168A pdb=" N VALLO 195 " --> pdb=" O LYSLO 191 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEULO 196 " --> pdb=" O TYRLO 192 " (cutoff:3.500A) Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 54 Processing helix chain 'LP' and resid 72 through 77 removed outlier: 4.554A pdb=" N TRPLP 76 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LP' and resid 84 through 106 Processing helix chain 'LQ' and resid 22 through 39 Processing helix chain 'LQ' and resid 41 through 54 removed outlier: 5.500A pdb=" N SERLQ 54 " --> pdb=" O ARGLQ 50 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 62 through 73 Proline residue: LQ 73 - end of helix Processing helix chain 'LQ' and resid 106 through 117 Processing helix chain 'LQ' and resid 122 through 130 Processing helix chain 'LQ' and resid 146 through 153 removed outlier: 5.644A pdb=" N GLYLQ 153 " --> pdb=" O TYRLQ 149 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 171 through 176 removed outlier: 5.179A pdb=" N GLULQ 175 " --> pdb=" O GLYLQ 171 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARGLQ 176 " --> pdb=" O ARGLQ 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 171 through 176' Processing helix chain 'LR' and resid 4 through 16 Processing helix chain 'LR' and resid 18 through 23 removed outlier: 5.723A pdb=" N TRPLR 23 " --> pdb=" O LYSLR 19 " (cutoff:3.500A) Processing helix chain 'LR' and resid 28 through 35 removed outlier: 4.474A pdb=" N ALALR 35 " --> pdb=" O GLULR 31 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 48 removed outlier: 5.956A pdb=" N ARGLR 42 " --> pdb=" O ARGLR 38 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 73 Processing helix chain 'LR' and resid 84 through 113 Proline residue: LR 90 - end of helix removed outlier: 6.672A pdb=" N VALLR 93 " --> pdb=" O METLR 89 " (cutoff:3.500A) Processing helix chain 'LR' and resid 116 through 130 Processing helix chain 'LR' and resid 134 through 188 removed outlier: 5.393A pdb=" N ILELR 184 " --> pdb=" O LYSLR 180 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILELR 185 " --> pdb=" O LYSLR 181 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYSLR 186 " --> pdb=" O GLULR 182 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THRLR 187 " --> pdb=" O GLULR 183 " (cutoff:3.500A) Processing helix chain 'LS' and resid 36 through 52 Processing helix chain 'LS' and resid 101 through 117 Processing helix chain 'LS' and resid 120 through 125 removed outlier: 5.264A pdb=" N GLNLS 125 " --> pdb=" O ALALS 121 " (cutoff:3.500A) Processing helix chain 'LS' and resid 139 through 147 removed outlier: 4.731A pdb=" N PHELS 145 " --> pdb=" O ALALS 141 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASPLS 147 " --> pdb=" O LYSLS 143 " (cutoff:3.500A) Processing helix chain 'LS' and resid 161 through 166 Proline residue: LS 165 - end of helix No H-bonds generated for 'chain 'LS' and resid 161 through 166' Processing helix chain 'LT' and resid 26 through 32 removed outlier: 4.251A pdb=" N TYRLT 30 " --> pdb=" O PROLT 26 " (cutoff:3.500A) Processing helix chain 'LT' and resid 54 through 59 removed outlier: 5.935A pdb=" N GLYLT 59 " --> pdb=" O LYSLT 55 " (cutoff:3.500A) Processing helix chain 'LT' and resid 92 through 97 removed outlier: 5.326A pdb=" N LYSLT 97 " --> pdb=" O ILELT 93 " (cutoff:3.500A) Processing helix chain 'LT' and resid 99 through 123 Processing helix chain 'LU' and resid 25 through 32 removed outlier: 4.395A pdb=" N VALLU 29 " --> pdb=" O CYSLU 25 " (cutoff:3.500A) Processing helix chain 'LU' and resid 35 through 47 Processing helix chain 'LU' and resid 55 through 60 Processing helix chain 'LU' and resid 79 through 95 Processing helix chain 'LV' and resid 69 through 74 removed outlier: 4.594A pdb=" N LYSLV 74 " --> pdb=" O PROLV 70 " (cutoff:3.500A) Processing helix chain 'LV' and resid 122 through 130 removed outlier: 4.349A pdb=" N LEULV 128 " --> pdb=" O GLULV 124 " (cutoff:3.500A) Proline residue: LV 130 - end of helix Processing helix chain 'LV' and resid 131 through 137 removed outlier: 3.761A pdb=" N ASNLV 135 " --> pdb=" O ARGLV 131 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLYLV 137 " --> pdb=" O ALALV 133 " (cutoff:3.500A) Processing helix chain 'LW' and resid 33 through 43 Processing helix chain 'LW' and resid 45 through 50 removed outlier: 5.354A pdb=" N ASNLW 50 " --> pdb=" O PROLW 46 " (cutoff:3.500A) Processing helix chain 'LW' and resid 52 through 60 Processing helix chain 'LW' and resid 86 through 96 removed outlier: 4.280A pdb=" N GLNLW 96 " --> pdb=" O ALALW 92 " (cutoff:3.500A) Processing helix chain 'LW' and resid 100 through 124 removed outlier: 4.671A pdb=" N GLNLW 104 " --> pdb=" O VALLW 100 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILELW 109 " --> pdb=" O ARGLW 105 " (cutoff:3.500A) Processing helix chain 'LX' and resid 72 through 78 removed outlier: 4.815A pdb=" N LYSLX 78 " --> pdb=" O TYRLX 74 " (cutoff:3.500A) Processing helix chain 'LX' and resid 83 through 93 Processing helix chain 'LX' and resid 105 through 117 Processing helix chain 'LX' and resid 145 through 154 Processing helix chain 'LY' and resid 10 through 21 Processing helix chain 'LY' and resid 22 through 31 Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 100 through 105 removed outlier: 5.361A pdb=" N VALLY 105 " --> pdb=" O PROLY 101 " (cutoff:3.500A) Processing helix chain 'LY' and resid 112 through 134 Processing helix chain 'LZ' and resid 58 through 67 removed outlier: 4.616A pdb=" N LYSLZ 67 " --> pdb=" O ALALZ 63 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 76 through 81 removed outlier: 5.033A pdb=" N METLZ 81 " --> pdb=" O TYRLZ 77 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 92 through 97 Processing helix chain 'LZ' and resid 103 through 125 removed outlier: 5.134A pdb=" N THRLZ 124 " --> pdb=" O GLULZ 120 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLYLZ 125 " --> pdb=" O ARGLZ 121 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 127 through 133 removed outlier: 5.174A pdb=" N LYSLZ 133 " --> pdb=" O TRPLZ 129 " (cutoff:3.500A) Processing helix chain 'La' and resid 6 through 12 Processing helix chain 'La' and resid 41 through 49 Processing helix chain 'La' and resid 64 through 69 removed outlier: 4.137A pdb=" N SERLa 68 " --> pdb=" O LYSLa 64 " (cutoff:3.500A) Processing helix chain 'La' and resid 74 through 83 removed outlier: 4.820A pdb=" N TRPLa 79 " --> pdb=" O LEULa 75 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THRLa 80 " --> pdb=" O ASPLa 76 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VALLa 82 " --> pdb=" O LEULa 78 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SERLa 83 " --> pdb=" O TRPLa 79 " (cutoff:3.500A) Processing helix chain 'La' and resid 84 through 93 Processing helix chain 'La' and resid 102 through 107 Processing helix chain 'La' and resid 130 through 141 Processing helix chain 'Lb' and resid 11 through 20 Processing helix chain 'Lb' and resid 36 through 51 removed outlier: 4.825A pdb=" N LYSLb 51 " --> pdb=" O LYSLb 47 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 53 through 74 removed outlier: 4.176A pdb=" N LYSLb 63 " --> pdb=" O ALALb 59 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 91 through 101 Processing helix chain 'Lb' and resid 105 through 118 Processing helix chain 'Lc' and resid 9 through 24 removed outlier: 4.892A pdb=" N LYSLc 23 " --> pdb=" O GLNLc 19 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 30 through 41 Processing helix chain 'Lc' and resid 53 through 68 Processing helix chain 'Lc' and resid 77 through 86 Processing helix chain 'Ld' and resid 28 through 34 Processing helix chain 'Ld' and resid 40 through 58 Processing helix chain 'Ld' and resid 65 through 74 Processing helix chain 'Le' and resid 24 through 29 removed outlier: 5.103A pdb=" N VALLe 29 " --> pdb=" O SERLe 25 " (cutoff:3.500A) Processing helix chain 'Le' and resid 43 through 48 Processing helix chain 'Le' and resid 81 through 89 removed outlier: 3.854A pdb=" N LEULe 88 " --> pdb=" O GLULe 84 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEULe 89 " --> pdb=" O LEULe 85 " (cutoff:3.500A) Processing helix chain 'Le' and resid 104 through 119 Processing helix chain 'Lf' and resid 35 through 43 removed outlier: 5.505A pdb=" N PHELf 41 " --> pdb=" O ASPLf 37 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYRLf 42 " --> pdb=" O GLULf 38 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEULf 43 " --> pdb=" O THRLf 39 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 60 through 68 removed outlier: 3.685A pdb=" N ARGLg 66 " --> pdb=" O LYSLg 62 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SERLg 68 " --> pdb=" O LEULg 64 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 83 through 112 Processing helix chain 'Lh' and resid 5 through 12 removed outlier: 5.267A pdb=" N GLYLh 11 " --> pdb=" O ARGLh 7 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYSLh 12 " --> pdb=" O ASPLh 8 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 13 through 38 Processing helix chain 'Lh' and resid 40 through 74 removed outlier: 4.605A pdb=" N ARGLh 48 " --> pdb=" O LEULh 44 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VALLh 49 " --> pdb=" O SERLh 45 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 80 through 85 Proline residue: Lh 85 - end of helix Processing helix chain 'Lh' and resid 88 through 95 removed outlier: 5.662A pdb=" N LEULh 95 " --> pdb=" O METLh 91 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 96 through 102 Processing helix chain 'Lh' and resid 104 through 114 Processing helix chain 'Li' and resid 25 through 30 removed outlier: 4.505A pdb=" N ARGLi 29 " --> pdb=" O ARGLi 25 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARGLi 30 " --> pdb=" O HISLi 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Li' and resid 25 through 30' Processing helix chain 'Li' and resid 34 through 49 Processing helix chain 'Li' and resid 51 through 64 Processing helix chain 'Li' and resid 65 through 78 Processing helix chain 'Li' and resid 79 through 103 Processing helix chain 'Lj' and resid 4 through 11 removed outlier: 4.337A pdb=" N ARGLj 11 " --> pdb=" O SERLj 7 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 Processing helix chain 'Lj' and resid 64 through 77 Processing helix chain 'Lk' and resid 7 through 17 Processing helix chain 'Lk' and resid 49 through 60 Processing helix chain 'Ll' and resid 6 through 21 removed outlier: 5.320A pdb=" N ARGLl 21 " --> pdb=" O GLNLl 17 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 24 through 31 removed outlier: 4.428A pdb=" N ARGLl 28 " --> pdb=" O PROLl 24 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N METLl 29 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THRLl 31 " --> pdb=" O ILELl 27 " (cutoff:3.500A) Processing helix chain 'Lm' and resid 79 through 91 Processing helix chain 'Ln' and resid 2 through 24 Processing helix chain 'Lo' and resid 35 through 46 Processing helix chain 'Lp' and resid 19 through 35 Processing helix chain 'Lp' and resid 73 through 92 removed outlier: 4.835A pdb=" N GLNLp 92 " --> pdb=" O GLULp 88 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 2 through 13 removed outlier: 5.828A pdb=" N ASNLr 12 " --> pdb=" O METLr 8 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYSLr 13 " --> pdb=" O VALLr 9 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 85 through 101 Processing helix chain 'Lr' and resid 103 through 123 removed outlier: 4.637A pdb=" N ARGLr 107 " --> pdb=" O ARGLr 103 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N METLr 108 " --> pdb=" O PROLr 104 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALALr 109 " --> pdb=" O ASPLr 105 " (cutoff:3.500A) Proline residue: Lr 123 - end of helix Processing helix chain 'Lz' and resid 73 through 81 removed outlier: 4.098A pdb=" N ALALz 79 " --> pdb=" O ASPLz 75 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VALLz 80 " --> pdb=" O GLULz 76 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 86 through 95 removed outlier: 5.326A pdb=" N LYSLz 95 " --> pdb=" O LYSLz 91 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 113 through 124 removed outlier: 5.193A pdb=" N ILELz 117 " --> pdb=" O SERLz 113 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYSLz 118 " --> pdb=" O GLULz 114 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLNLz 119 " --> pdb=" O SERLz 115 " (cutoff:3.500A) Proline residue: Lz 121 - end of helix removed outlier: 3.637A pdb=" N LEULz 124 " --> pdb=" O ILELz 120 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 126 through 132 Processing helix chain 'Lz' and resid 176 through 183 removed outlier: 5.431A pdb=" N TYRLz 181 " --> pdb=" O ASPLz 177 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 185 through 194 removed outlier: 5.212A pdb=" N LEULz 193 " --> pdb=" O PHELz 189 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEULz 194 " --> pdb=" O LEULz 190 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'LA' and resid 47 through 50 removed outlier: 6.607A pdb=" N LYSLA 60 " --> pdb=" O LYSLA 46 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLNLA 86 " --> pdb=" O VALLA 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'LA' and resid 110 through 114 removed outlier: 6.703A pdb=" N ARGLA 147 " --> pdb=" O ILELA 137 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SERLA 138 " --> pdb=" O ARGLA 147 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'LA' and resid 58 through 65 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'LA' and resid 145 through 150 Processing sheet with id= 5, first strand: chain 'LB' and resid 41 through 44 removed outlier: 6.614A pdb=" N GLNLB 184 " --> pdb=" O THRLB 44 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HISLB 179 " --> pdb=" O THRLB 166 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILELB 160 " --> pdb=" O VALLB 185 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLYLB 187 " --> pdb=" O GLNLB 158 " (cutoff:3.500A) removed outlier: 13.592A pdb=" N GLNLB 158 " --> pdb=" O GLYLB 187 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLYLB 91 " --> pdb=" O PHELB 102 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'LB' and resid 53 through 59 removed outlier: 6.771A pdb=" N ILELB 78 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARGLB 343 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VALLB 344 " --> pdb=" O VALLB 222 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VALLB 222 " --> pdb=" O VALLB 344 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'LB' and resid 84 through 87 Processing sheet with id= 8, first strand: chain 'LB' and resid 286 through 290 removed outlier: 4.472A pdb=" N PHELB 330 " --> pdb=" O GLYLB 288 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLYLB 290 " --> pdb=" O ASNLB 328 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASNLB 328 " --> pdb=" O GLYLB 290 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'LB' and resid 76 through 80 No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'LB' and resid 88 through 91 removed outlier: 3.564A pdb=" N LYSLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LB' and resid 214 through 218 removed outlier: 4.407A pdb=" N GLULB 215 " --> pdb=" O ILELB 284 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LC' and resid 6 through 9 Processing sheet with id= 13, first strand: chain 'LC' and resid 226 through 231 removed outlier: 6.274A pdb=" N TYRLC 211 " --> pdb=" O LEULC 230 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N PHELC 249 " --> pdb=" O GLYLC 206 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LD' and resid 60 through 66 Processing sheet with id= 15, first strand: chain 'LE' and resid 91 through 96 removed outlier: 4.882A pdb=" N VALLE 96 " --> pdb=" O GLYLE 103 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLYLE 103 " --> pdb=" O VALLE 96 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LE' and resid 148 through 153 removed outlier: 4.477A pdb=" N THRLE 148 " --> pdb=" O PHELE 164 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LF' and resid 139 through 144 removed outlier: 7.548A pdb=" N TYRLF 139 " --> pdb=" O ILELF 95 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHELF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LF' and resid 158 through 162 removed outlier: 6.517A pdb=" N GLYLF 158 " --> pdb=" O LEULF 169 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LG' and resid 180 through 185 Processing sheet with id= 20, first strand: chain 'LH' and resid 5 through 12 removed outlier: 6.106A pdb=" N SERLH 6 " --> pdb=" O LYSLH 59 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYSLH 53 " --> pdb=" O ILELH 12 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARGLH 54 " --> pdb=" O LEULH 48 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LH' and resid 17 through 20 Processing sheet with id= 22, first strand: chain 'LH' and resid 102 through 106 removed outlier: 6.331A pdb=" N ASNLH 102 " --> pdb=" O ARGLH 115 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SERLH 110 " --> pdb=" O METLH 128 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LH' and resid 132 through 137 removed outlier: 5.966A pdb=" N GLULH 143 " --> pdb=" O SERLH 137 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASPLH 142 " --> pdb=" O SERLH 94 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LH' and resid 87 through 92 removed outlier: 4.697A pdb=" N GLYLH 87 " --> pdb=" O VALLH 187 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LI' and resid 34 through 37 removed outlier: 6.403A pdb=" N PHELI 34 " --> pdb=" O VALLI 89 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILELI 135 " --> pdb=" O ARGLI 90 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLYLI 49 " --> pdb=" O SERLI 168 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARGLI 162 " --> pdb=" O ASPLI 55 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LI' and resid 189 through 192 removed outlier: 5.442A pdb=" N CYSLI 189 " --> pdb=" O VALLI 200 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LJ' and resid 48 through 52 removed outlier: 4.883A pdb=" N ILELJ 68 " --> pdb=" O VALLJ 26 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VALLJ 74 " --> pdb=" O LEULJ 20 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N CYSLJ 25 " --> pdb=" O GLYLJ 127 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLYLJ 127 " --> pdb=" O CYSLJ 25 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LM' and resid 11 through 16 removed outlier: 4.356A pdb=" N ARGLM 11 " --> pdb=" O ILELM 27 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LN' and resid 35 through 39 removed outlier: 6.567A pdb=" N ALALN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THRLN 126 " --> pdb=" O ARGLN 68 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LN' and resid 117 through 121 removed outlier: 3.583A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHELN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LO' and resid 6 through 10 Processing sheet with id= 32, first strand: chain 'LP' and resid 13 through 20 removed outlier: 6.906A pdb=" N LYSLP 13 " --> pdb=" O GLULP 152 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILELP 149 " --> pdb=" O GLULP 115 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SERLP 111 " --> pdb=" O LYSLP 153 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.145A pdb=" N GLNLP 80 " --> pdb=" O PHELP 60 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LP' and resid 116 through 122 Processing sheet with id= 35, first strand: chain 'LP' and resid 124 through 132 removed outlier: 4.013A pdb=" N METLP 125 " --> pdb=" O SERLP 141 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARGLP 127 " --> pdb=" O TYRLP 139 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LQ' and resid 78 through 82 Processing sheet with id= 37, first strand: chain 'LQ' and resid 98 through 101 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'LS' and resid 27 through 33 removed outlier: 6.607A pdb=" N VALLS 13 " --> pdb=" O VALLS 62 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N SERLS 58 " --> pdb=" O LEULS 17 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LS' and resid 91 through 99 Processing sheet with id= 40, first strand: chain 'LS' and resid 9 through 13 removed outlier: 4.739A pdb=" N GLULS 9 " --> pdb=" O VALLS 67 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LT' and resid 38 through 42 removed outlier: 4.397A pdb=" N ASPLT 38 " --> pdb=" O VALLT 64 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LU' and resid 21 through 24 removed outlier: 7.195A pdb=" N TRPLU 99 " --> pdb=" O PHELU 115 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LU' and resid 61 through 65 Processing sheet with id= 44, first strand: chain 'LV' and resid 36 through 39 removed outlier: 4.676A pdb=" N ALALV 24 " --> pdb=" O ILELV 39 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASNLV 101 " --> pdb=" O VALLV 25 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILELV 105 " --> pdb=" O ALALV 29 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASPLV 59 " --> pdb=" O VALLV 81 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LV' and resid 87 through 90 removed outlier: 5.659A pdb=" N VALLV 94 " --> pdb=" O ARGLV 90 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LV' and resid 82 through 85 removed outlier: 6.720A pdb=" N ASPLV 100 " --> pdb=" O ARGLV 85 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LW' and resid 3 through 6 removed outlier: 6.672A pdb=" N GLULW 4 " --> pdb=" O LYSLW 12 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYSLW 12 " --> pdb=" O GLULW 4 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N CYSLW 6 " --> pdb=" O GLYLW 10 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'LW' and resid 18 through 23 removed outlier: 4.270A pdb=" N LYSLW 27 " --> pdb=" O ARGLW 23 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LX' and resid 95 through 100 removed outlier: 4.437A pdb=" N GLULX 133 " --> pdb=" O ARGLX 129 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'LY' and resid 53 through 56 removed outlier: 4.643A pdb=" N ASPLY 53 " --> pdb=" O VALLY 70 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'LY' and resid 71 through 75 Processing sheet with id= 52, first strand: chain 'LY' and resid 85 through 88 removed outlier: 6.132A pdb=" N VALLY 85 " --> pdb=" O VALLY 97 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'LZ' and resid 9 through 14 removed outlier: 4.488A pdb=" N LYSLZ 9 " --> pdb=" O ILELZ 25 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HISLZ 40 " --> pdb=" O ILELZ 29 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'LZ' and resid 42 through 45 Processing sheet with id= 55, first strand: chain 'La' and resid 98 through 101 Processing sheet with id= 56, first strand: chain 'Lc' and resid 26 through 29 removed outlier: 6.925A pdb=" N LYSLc 26 " --> pdb=" O ILELc 97 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASNLc 50 " --> pdb=" O TYRLc 74 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Ld' and resid 61 through 64 removed outlier: 5.880A pdb=" N ASPLd 61 " --> pdb=" O LEULd 102 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THRLd 22 " --> pdb=" O VALLd 122 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Le' and resid 74 through 80 Processing sheet with id= 59, first strand: chain 'Lf' and resid 56 through 60 removed outlier: 5.955A pdb=" N THRLf 57 " --> pdb=" O PROLf 64 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THRLf 59 " --> pdb=" O GLYLf 62 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Lf' and resid 9 through 12 removed outlier: 6.679A pdb=" N LEULf 27 " --> pdb=" O ALALf 12 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARGLf 85 " --> pdb=" O THRLf 75 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYSLf 45 " --> pdb=" O VALLf 74 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARGLf 46 " --> pdb=" O METLf 104 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Lf' and resid 6 through 12 removed outlier: 4.222A pdb=" N HISLf 99 " --> pdb=" O PHELf 11 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Lg' and resid 20 through 24 Processing sheet with id= 63, first strand: chain 'Lk' and resid 2 through 5 removed outlier: 4.529A pdb=" N VALLk 46 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYSLk 27 " --> pdb=" O LEULk 69 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Lm' and resid 93 through 96 removed outlier: 5.774A pdb=" N LYSLm 93 " --> pdb=" O LYSLm 124 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Lo' and resid 6 through 10 removed outlier: 5.266A pdb=" N LYSLo 6 " --> pdb=" O VALLo 23 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VALLo 67 " --> pdb=" O TYRLo 26 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Lp' and resid 47 through 50 removed outlier: 6.895A pdb=" N ILELp 54 " --> pdb=" O ARGLp 50 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLYLp 53 " --> pdb=" O GLYLp 66 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'Lr' and resid 48 through 53 removed outlier: 5.132A pdb=" N THRLr 48 " --> pdb=" O LYSLr 65 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SERLr 76 " --> pdb=" O ARGLr 66 " (cutoff:3.500A) 2260 hydrogen bonds defined for protein. 6696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3315 hydrogen bonds 5522 hydrogen bond angles 0 basepair planarities 1277 basepair parallelities 2073 stacking parallelities Total time for adding SS restraints: 312.87 Time building geometry restraints manager: 59.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 13597 1.30 - 1.43: 64970 1.43 - 1.56: 64816 1.56 - 1.69: 8098 1.69 - 1.82: 394 Bond restraints: 151875 Sorted by residual: bond pdb=" C20 OCWL55315 " pdb=" C21 OCWL55315 " ideal model delta sigma weight residual 1.562 1.301 0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C15 OCWL55315 " pdb=" C17 OCWL55315 " ideal model delta sigma weight residual 1.589 1.484 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C17 OCWL55315 " pdb=" C18 OCWL55315 " ideal model delta sigma weight residual 1.448 1.344 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C GLYLH 32 " pdb=" O GLYLH 32 " ideal model delta sigma weight residual 1.236 1.214 0.022 5.30e-03 3.56e+04 1.78e+01 bond pdb=" C16 OCWL55315 " pdb=" C18 OCWL55315 " ideal model delta sigma weight residual 1.585 1.504 0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 151870 not shown) Histogram of bond angle deviations from ideal: 94.86 - 103.33: 9796 103.33 - 111.80: 85907 111.80 - 120.27: 74253 120.27 - 128.74: 50173 128.74 - 137.20: 4313 Bond angle restraints: 224442 Sorted by residual: angle pdb=" C24 OCWL55315 " pdb=" C26 OCWL55315 " pdb=" C31 OCWL55315 " ideal model delta sigma weight residual 97.60 123.43 -25.83 3.00e+00 1.11e-01 7.42e+01 angle pdb=" C18 OCWL55315 " pdb=" C22 OCWL55315 " pdb=" O08 OCWL55315 " ideal model delta sigma weight residual 93.38 116.01 -22.63 3.00e+00 1.11e-01 5.69e+01 angle pdb=" C ALALM 87 " pdb=" N ALALM 88 " pdb=" CA ALALM 88 " ideal model delta sigma weight residual 121.54 134.61 -13.07 1.91e+00 2.74e-01 4.69e+01 angle pdb=" C ALALC 2 " pdb=" N CYSLC 3 " pdb=" CA CYSLC 3 " ideal model delta sigma weight residual 121.70 133.68 -11.98 1.80e+00 3.09e-01 4.43e+01 angle pdb=" N TYRLC 277 " pdb=" CA TYRLC 277 " pdb=" C TYRLC 277 " ideal model delta sigma weight residual 109.07 119.76 -10.69 1.61e+00 3.86e-01 4.41e+01 ... (remaining 224437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 86401 36.00 - 72.00: 10752 72.00 - 108.00: 1280 108.00 - 144.00: 22 144.00 - 180.00: 44 Dihedral angle restraints: 98499 sinusoidal: 78847 harmonic: 19652 Sorted by residual: dihedral pdb=" CA LEULB 17 " pdb=" C LEULB 17 " pdb=" N PROLB 18 " pdb=" CA PROLB 18 " ideal model delta harmonic sigma weight residual 180.00 91.73 88.27 0 5.00e+00 4.00e-02 3.12e+02 dihedral pdb=" CA TYRLj 39 " pdb=" C TYRLj 39 " pdb=" N PROLj 40 " pdb=" CA PROLj 40 " ideal model delta harmonic sigma weight residual 180.00 95.68 84.32 0 5.00e+00 4.00e-02 2.84e+02 dihedral pdb=" CA TYRLf 106 " pdb=" C TYRLf 106 " pdb=" N PROLf 107 " pdb=" CA PROLf 107 " ideal model delta harmonic sigma weight residual -180.00 -112.69 -67.31 0 5.00e+00 4.00e-02 1.81e+02 ... (remaining 98496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.090: 28023 1.090 - 2.179: 0 2.179 - 3.269: 0 3.269 - 4.358: 0 4.358 - 5.448: 2 Chirality restraints: 28025 Sorted by residual: chirality pdb=" C12 OCWL55315 " pdb=" C13 OCWL55315 " pdb=" C14 OCWL55315 " pdb=" C15 OCWL55315 " both_signs ideal model delta sigma weight residual False -2.65 2.80 -5.45 2.00e-01 2.50e+01 7.42e+02 chirality pdb=" C13 OCWL55315 " pdb=" C12 OCWL55315 " pdb=" C16 OCWL55315 " pdb=" C19 OCWL55315 " both_signs ideal model delta sigma weight residual False -2.65 2.78 -5.43 2.00e-01 2.50e+01 7.36e+02 chirality pdb=" CG LEULQ 128 " pdb=" CB LEULQ 128 " pdb=" CD1 LEULQ 128 " pdb=" CD2 LEULQ 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.19e+00 ... (remaining 28022 not shown) Planarity restraints: 13439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CL5 456 " -0.066 2.00e-02 2.50e+03 4.15e-02 3.87e+01 pdb=" N1 CL5 456 " 0.081 2.00e-02 2.50e+03 pdb=" C2 CL5 456 " -0.048 2.00e-02 2.50e+03 pdb=" O2 CL5 456 " 0.042 2.00e-02 2.50e+03 pdb=" N3 CL5 456 " -0.010 2.00e-02 2.50e+03 pdb=" C4 CL5 456 " -0.008 2.00e-02 2.50e+03 pdb=" N4 CL5 456 " -0.012 2.00e-02 2.50e+03 pdb=" C5 CL5 456 " 0.006 2.00e-02 2.50e+03 pdb=" C6 CL5 456 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GL5 417 " -0.076 2.00e-02 2.50e+03 3.46e-02 3.60e+01 pdb=" N9 GL5 417 " 0.087 2.00e-02 2.50e+03 pdb=" C8 GL5 417 " 0.006 2.00e-02 2.50e+03 pdb=" N7 GL5 417 " -0.001 2.00e-02 2.50e+03 pdb=" C5 GL5 417 " -0.008 2.00e-02 2.50e+03 pdb=" C6 GL5 417 " -0.015 2.00e-02 2.50e+03 pdb=" O6 GL5 417 " -0.009 2.00e-02 2.50e+03 pdb=" N1 GL5 417 " -0.009 2.00e-02 2.50e+03 pdb=" C2 GL5 417 " 0.003 2.00e-02 2.50e+03 pdb=" N2 GL5 417 " 0.006 2.00e-02 2.50e+03 pdb=" N3 GL5 417 " 0.021 2.00e-02 2.50e+03 pdb=" C4 GL5 417 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CL51082 " 0.055 2.00e-02 2.50e+03 3.99e-02 3.57e+01 pdb=" N1 CL51082 " -0.072 2.00e-02 2.50e+03 pdb=" C2 CL51082 " 0.059 2.00e-02 2.50e+03 pdb=" O2 CL51082 " -0.045 2.00e-02 2.50e+03 pdb=" N3 CL51082 " -0.002 2.00e-02 2.50e+03 pdb=" C4 CL51082 " 0.017 2.00e-02 2.50e+03 pdb=" N4 CL51082 " 0.005 2.00e-02 2.50e+03 pdb=" C5 CL51082 " -0.006 2.00e-02 2.50e+03 pdb=" C6 CL51082 " -0.012 2.00e-02 2.50e+03 ... (remaining 13436 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 969 2.51 - 3.11: 90052 3.11 - 3.71: 268492 3.71 - 4.30: 392097 4.30 - 4.90: 536917 Nonbonded interactions: 1288527 Sorted by model distance: nonbonded pdb=" O PHELU 115 " pdb=" O GLNLU 116 " model vdw 1.914 3.040 nonbonded pdb=" OP1 AL53642 " pdb="MG MGL55174 " model vdw 1.967 2.170 nonbonded pdb=" OP2 UL53645 " pdb="MG MGL55174 " model vdw 1.990 2.170 nonbonded pdb=" O6 GL51321 " pdb="MG MGL55143 " model vdw 1.995 2.170 nonbonded pdb=" OP1 CL54375 " pdb="MG MGL55179 " model vdw 1.995 2.170 ... (remaining 1288522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 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: 0.110 Extract box with map and model: 21.890 Check model and map are aligned: 1.510 Set scattering table: 0.940 Process input model: 610.520 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 653.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.261 151875 Z= 0.410 Angle : 1.015 25.834 224442 Z= 0.526 Chirality : 0.070 5.448 28025 Planarity : 0.008 0.126 13439 Dihedral : 24.049 179.997 85823 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.02 % Favored : 92.68 % Rotamer: Outliers : 0.96 % Allowed : 8.56 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.17 % Twisted Proline : 1.77 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.09), residues: 6696 helix: -1.16 (0.09), residues: 2402 sheet: -1.58 (0.16), residues: 908 loop : -2.49 (0.09), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRPLb 16 HIS 0.037 0.003 HISLB 258 PHE 0.041 0.003 PHELU 39 TYR 0.027 0.003 TYRLQ 32 ARG 0.022 0.001 ARGLD 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1851 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1796 time to evaluate : 6.667 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: LA 204 MET cc_start: 0.8771 (mtt) cc_final: 0.8561 (mtt) REVERT: LB 17 LEU cc_start: 0.8112 (pt) cc_final: 0.7821 (pt) REVERT: LC 101 MET cc_start: 0.8813 (ptm) cc_final: 0.8484 (ptm) REVERT: LE 91 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8111 (p) REVERT: LG 148 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7236 (mt-10) REVERT: LJ 170 TYR cc_start: 0.7165 (m-80) cc_final: 0.6807 (m-80) REVERT: LM 50 MET cc_start: 0.7822 (ttm) cc_final: 0.7521 (ttm) REVERT: LM 82 ILE cc_start: 0.8755 (mm) cc_final: 0.8512 (mm) REVERT: LS 6 THR cc_start: 0.8203 (t) cc_final: 0.7933 (m) REVERT: LW 45 ASN cc_start: 0.8443 (t0) cc_final: 0.8239 (t0) REVERT: Le 90 MET cc_start: 0.8397 (mmm) cc_final: 0.7741 (mmp) REVERT: Lg 15 THR cc_start: 0.9340 (p) cc_final: 0.9138 (p) REVERT: Lh 62 ASN cc_start: 0.8372 (m-40) cc_final: 0.8167 (m110) REVERT: Lh 64 THR cc_start: 0.8553 (p) cc_final: 0.8326 (p) REVERT: Lm 94 MET cc_start: 0.8332 (mmm) cc_final: 0.8107 (mmm) REVERT: Ln 1 MET cc_start: 0.6277 (mtp) cc_final: 0.5978 (mpm) REVERT: Ln 11 ARG cc_start: 0.7625 (mtt180) cc_final: 0.7361 (ttt-90) REVERT: Ln 21 ARG cc_start: 0.8731 (mtp180) cc_final: 0.6797 (tpt170) REVERT: Lo 34 TYR cc_start: 0.8441 (m-80) cc_final: 0.8167 (m-80) REVERT: Lo 66 ILE cc_start: 0.8515 (mt) cc_final: 0.8048 (mp) REVERT: Lp 33 GLN cc_start: 0.8494 (tt0) cc_final: 0.8140 (tt0) REVERT: Lr 102 TYR cc_start: 0.8831 (t80) cc_final: 0.8520 (t80) REVERT: Lz 144 MET cc_start: 0.0781 (mtt) cc_final: 0.0014 (mmt) REVERT: Lz 159 MET cc_start: -0.1306 (mmt) cc_final: -0.1803 (tpt) REVERT: Lz 197 ASN cc_start: 0.0691 (OUTLIER) cc_final: 0.0075 (m-40) outliers start: 55 outliers final: 25 residues processed: 1834 average time/residue: 2.3380 time to fit residues: 6037.8977 Evaluate side-chains 1282 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1255 time to evaluate : 6.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 4 VAL Chi-restraints excluded: chain LA residue 15 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LE residue 91 THR Chi-restraints excluded: chain LE residue 186 LEU Chi-restraints excluded: chain LE residue 264 ILE Chi-restraints excluded: chain LH residue 57 VAL Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 38 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LO residue 150 GLN Chi-restraints excluded: chain LQ residue 83 VAL Chi-restraints excluded: chain LS residue 85 ASP Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LU residue 19 LEU Chi-restraints excluded: chain LV residue 65 VAL Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 20 ASN Chi-restraints excluded: chain LY residue 118 ILE Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain Le residue 94 SER Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lp residue 29 ILE Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lz residue 148 VAL Chi-restraints excluded: chain Lz residue 197 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 896 optimal weight: 0.9990 chunk 804 optimal weight: 4.9990 chunk 446 optimal weight: 0.9980 chunk 274 optimal weight: 50.0000 chunk 542 optimal weight: 0.9980 chunk 430 optimal weight: 3.9990 chunk 832 optimal weight: 8.9990 chunk 322 optimal weight: 6.9990 chunk 506 optimal weight: 4.9990 chunk 619 optimal weight: 5.9990 chunk 964 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 132 ASN LA 140 ASN ** LA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 216 HIS LB 145 GLN LB 204 GLN LB 209 GLN LB 354 GLN LC 38 ASN LC 43 ASN LC 50 GLN LC 198 ASN ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 111 ASN LD 191 ASN ** LD 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 282 GLN LE 167 GLN LE 190 HIS LE 191 GLN LE 227 HIS LF 39 GLN LG 46 GLN LG 100 HIS LG 159 HIS LG 227 ASN LH 39 ASN LH 78 GLN LH 163 GLN LI 133 GLN LI 177 ASN LI 203 HIS LJ 10 ASN LJ 23 ASN LJ 42 GLN LJ 46 GLN LJ 112 HIS LL 104 ASN LL 175 ASN LM 34 ASN LM 75 GLN LM 125 ASN LN 99 GLN LN 196 ASN LN 199 GLN LO 167 HIS LP 25 HIS LP 56 GLN LP 97 ASN LP 116 HIS ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 44 ASN ** LQ 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 86 ASN LS 50 GLN ** LS 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 125 GLN LT 127 GLN LU 27 HIS LU 95 ASN ** LV 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 36 ASN LV 77 HIS LW 17 HIS LW 33 ASN LW 48 GLN ** LW 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 125 ASN LY 4 ASN LY 127 GLN LZ 78 ASN La 28 HIS La 85 GLN La 93 ASN La 120 GLN Lb 7 HIS ** Lb 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lc 33 GLN Ld 18 ASN Ld 116 ASN Le 43 ASN Lf 56 ASN Lf 80 ASN Lh 20 GLN Lh 101 ASN Lh 108 GLN Li 20 ASN Li 36 HIS Lj 66 HIS Lm 90 ASN Lm 117 HIS Lm 120 ASN Lo 19 GLN Lo 45 GLN Lp 56 HIS Lr 6 GLN Lr 70 GLN Lr 100 ASN Lr 121 GLN Lz 71 GLN Lz 129 ASN ** Lz 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lz 197 ASN Total number of N/Q/H flips: 93 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 151875 Z= 0.196 Angle : 0.627 27.790 224442 Z= 0.317 Chirality : 0.041 2.678 28025 Planarity : 0.005 0.096 13439 Dihedral : 24.661 179.423 71487 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.27 % Favored : 93.62 % Rotamer: Outliers : 3.95 % Allowed : 18.52 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.17 % Twisted Proline : 1.77 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.10), residues: 6696 helix: 0.33 (0.10), residues: 2425 sheet: -1.19 (0.16), residues: 885 loop : -1.92 (0.10), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPLb 16 HIS 0.013 0.001 HISLE 128 PHE 0.019 0.001 PHELZ 131 TYR 0.019 0.002 TYRLU 82 ARG 0.012 0.001 ARGLC 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1629 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1402 time to evaluate : 6.749 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: LB 17 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7769 (pt) REVERT: LB 224 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8211 (mtpt) REVERT: LC 101 MET cc_start: 0.8777 (ptm) cc_final: 0.8406 (ptm) REVERT: LC 300 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7612 (ttp-170) REVERT: LD 208 MET cc_start: 0.7793 (mtp) cc_final: 0.7506 (mtm) REVERT: LE 91 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.8060 (p) REVERT: LF 33 LEU cc_start: 0.8964 (tt) cc_final: 0.8662 (tp) REVERT: LH 37 ASP cc_start: 0.7181 (t0) cc_final: 0.6929 (t0) REVERT: LM 33 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7003 (tp40) REVERT: LN 189 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7997 (ptm-80) REVERT: LO 78 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7851 (mmp-170) REVERT: LO 173 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7314 (tp-100) REVERT: LQ 83 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8688 (t) REVERT: LR 28 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6727 (mm-30) REVERT: LT 120 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7854 (tptp) REVERT: La 92 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7764 (pttm) REVERT: Lc 45 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8467 (tm) REVERT: Lc 61 GLU cc_start: 0.6977 (tp30) cc_final: 0.6705 (tp30) REVERT: Le 90 MET cc_start: 0.8265 (mmm) cc_final: 0.7781 (mmp) REVERT: Lk 8 ILE cc_start: 0.8521 (mm) cc_final: 0.8156 (mm) REVERT: Lm 94 MET cc_start: 0.8263 (mmm) cc_final: 0.8015 (mmm) REVERT: Ln 1 MET cc_start: 0.6402 (mtp) cc_final: 0.6138 (mpm) REVERT: Ln 11 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7089 (tpt-90) REVERT: Ln 17 ARG cc_start: 0.8918 (mtm-85) cc_final: 0.8713 (mtt180) REVERT: Ln 21 ARG cc_start: 0.8841 (mtp180) cc_final: 0.6912 (tpt170) REVERT: Lp 10 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8828 (tp) REVERT: Lp 33 GLN cc_start: 0.8505 (tt0) cc_final: 0.8168 (tt0) REVERT: Lz 78 LYS cc_start: 0.3946 (mmpt) cc_final: 0.3331 (mmtt) REVERT: Lz 144 MET cc_start: 0.1251 (mtt) cc_final: 0.0302 (mmt) outliers start: 227 outliers final: 82 residues processed: 1504 average time/residue: 2.1038 time to fit residues: 4562.0221 Evaluate side-chains 1343 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1250 time to evaluate : 6.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 4 VAL Chi-restraints excluded: chain LA residue 15 VAL Chi-restraints excluded: chain LA residue 75 LEU Chi-restraints excluded: chain LA residue 102 LEU Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LA residue 175 ILE Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 17 LEU Chi-restraints excluded: chain LB residue 216 MET Chi-restraints excluded: chain LB residue 224 LYS Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LC residue 300 ARG Chi-restraints excluded: chain LC residue 334 THR Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LD residue 112 ARG Chi-restraints excluded: chain LD residue 126 THR Chi-restraints excluded: chain LD residue 194 VAL Chi-restraints excluded: chain LD residue 232 THR Chi-restraints excluded: chain LE residue 88 VAL Chi-restraints excluded: chain LE residue 91 THR Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LG residue 156 VAL Chi-restraints excluded: chain LG residue 192 ARG Chi-restraints excluded: chain LH residue 94 SER Chi-restraints excluded: chain LI residue 35 ASP Chi-restraints excluded: chain LI residue 43 VAL Chi-restraints excluded: chain LI residue 79 SER Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 100 SER Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 133 VAL Chi-restraints excluded: chain LL residue 109 SER Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 33 GLN Chi-restraints excluded: chain LM residue 38 VAL Chi-restraints excluded: chain LM residue 70 GLN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 189 ARG Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 64 THR Chi-restraints excluded: chain LO residue 78 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 141 LEU Chi-restraints excluded: chain LP residue 85 LYS Chi-restraints excluded: chain LQ residue 79 THR Chi-restraints excluded: chain LQ residue 83 VAL Chi-restraints excluded: chain LR residue 30 ASN Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LS residue 85 ASP Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LT residue 29 THR Chi-restraints excluded: chain LT residue 120 LYS Chi-restraints excluded: chain LU residue 102 VAL Chi-restraints excluded: chain LV residue 65 VAL Chi-restraints excluded: chain LV residue 94 VAL Chi-restraints excluded: chain LV residue 118 THR Chi-restraints excluded: chain LW residue 54 LEU Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LZ residue 19 SER Chi-restraints excluded: chain LZ residue 95 VAL Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lc residue 45 LEU Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 100 ASN Chi-restraints excluded: chain Le residue 34 ASN Chi-restraints excluded: chain Le residue 45 VAL Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 76 ARG Chi-restraints excluded: chain Lg residue 2 VAL Chi-restraints excluded: chain Lg residue 48 VAL Chi-restraints excluded: chain Lh residue 116 LEU Chi-restraints excluded: chain Lk residue 66 VAL Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Lm residue 84 GLN Chi-restraints excluded: chain Ln residue 10 MET Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lp residue 10 ILE Chi-restraints excluded: chain Lp residue 63 THR Chi-restraints excluded: chain Lp residue 81 SER Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 60 VAL Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 148 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 535 optimal weight: 20.0000 chunk 299 optimal weight: 7.9990 chunk 802 optimal weight: 4.9990 chunk 656 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 chunk 966 optimal weight: 0.7980 chunk 1043 optimal weight: 5.9990 chunk 860 optimal weight: 8.9990 chunk 958 optimal weight: 8.9990 chunk 329 optimal weight: 7.9990 chunk 775 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 50 HIS LA 132 ASN ** LA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 42 HIS LB 213 GLN LC 43 ASN LC 61 GLN ** LC 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 202 GLN LE 256 GLN LF 63 GLN LF 131 ASN LG 46 GLN LG 100 HIS LG 159 HIS ** LH 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 163 GLN LI 133 GLN LI 213 HIS LJ 46 GLN LJ 167 GLN LL 40 GLN LM 75 GLN LN 99 GLN LN 199 GLN LO 184 ASN LP 40 HIS LP 137 ASN LQ 160 HIS LR 130 ASN LS 50 GLN ** LS 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 122 HIS LS 125 GLN LT 127 GLN LU 27 HIS LU 95 ASN ** LV 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LW 59 HIS ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 111 GLN LY 43 ASN LY 127 GLN LZ 78 ASN La 67 GLN La 85 GLN La 120 GLN Lb 19 ASN Lb 50 ASN Lb 60 ASN Ld 79 ASN Le 23 HIS Lh 20 GLN Lh 65 GLN Lh 108 GLN Li 20 ASN Li 26 HIS Li 36 HIS Lm 109 ASN Lm 120 ASN Ln 22 GLN Lo 25 GLN Lo 102 GLN Lr 100 ASN Lr 121 GLN Lz 40 ASN Lz 143 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 151875 Z= 0.468 Angle : 0.762 23.867 224442 Z= 0.385 Chirality : 0.049 2.620 28025 Planarity : 0.007 0.105 13439 Dihedral : 24.724 179.979 71468 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.77 % Favored : 93.09 % Rotamer: Outliers : 5.57 % Allowed : 19.10 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.17 % Twisted Proline : 1.77 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.10), residues: 6696 helix: 0.54 (0.10), residues: 2434 sheet: -1.11 (0.16), residues: 932 loop : -1.64 (0.10), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRPLC 67 HIS 0.016 0.002 HISLE 128 PHE 0.036 0.002 PHELD 3 TYR 0.027 0.003 TYRLQ 32 ARG 0.012 0.001 ARGLZ 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1684 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1364 time to evaluate : 6.830 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: LA 141 PRO cc_start: 0.8850 (Cg_endo) cc_final: 0.8146 (Cg_exo) REVERT: LA 208 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7881 (pm20) REVERT: LB 17 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7710 (pt) REVERT: LB 70 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8573 (mtpp) REVERT: LB 351 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8035 (pp) REVERT: LB 360 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8107 (pp) REVERT: LD 208 MET cc_start: 0.8130 (mtp) cc_final: 0.7886 (mtm) REVERT: LD 271 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8163 (ttp) REVERT: LE 62 MET cc_start: 0.8888 (mmm) cc_final: 0.8457 (mmt) REVERT: LE 249 ASP cc_start: 0.7767 (m-30) cc_final: 0.6443 (m-30) REVERT: LF 33 LEU cc_start: 0.8966 (tt) cc_final: 0.8726 (tp) REVERT: LH 58 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: LH 142 ASP cc_start: 0.7542 (p0) cc_final: 0.7326 (p0) REVERT: LL 129 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7500 (mmm-85) REVERT: LM 33 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7253 (tp40) REVERT: LM 50 MET cc_start: 0.7916 (ttm) cc_final: 0.7610 (ttm) REVERT: LN 153 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8691 (mptt) REVERT: LO 78 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7937 (mmt180) REVERT: LQ 128 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8859 (mm) REVERT: LR 28 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6967 (mm-30) REVERT: LS 69 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: LS 80 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9027 (mm) REVERT: LT 120 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7760 (tptp) REVERT: LW 1 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.6393 (tmm) REVERT: LW 11 TYR cc_start: 0.8455 (m-80) cc_final: 0.8241 (m-80) REVERT: La 106 SER cc_start: 0.8828 (m) cc_final: 0.8466 (m) REVERT: Lc 61 GLU cc_start: 0.7075 (tp30) cc_final: 0.6688 (tp30) REVERT: Ld 33 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8400 (tp) REVERT: Lh 87 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7497 (mtpt) REVERT: Lj 10 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8219 (mttm) REVERT: Ll 35 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8760 (mt) REVERT: Lm 94 MET cc_start: 0.8353 (mmm) cc_final: 0.8080 (mmm) REVERT: Ln 11 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7312 (tpt-90) REVERT: Ln 17 ARG cc_start: 0.8942 (mtm-85) cc_final: 0.8629 (mtt180) REVERT: Ln 21 ARG cc_start: 0.8971 (mtp180) cc_final: 0.6882 (tpt170) REVERT: Lr 52 GLU cc_start: 0.7830 (mp0) cc_final: 0.7593 (mp0) REVERT: Lz 78 LYS cc_start: 0.3754 (mmpt) cc_final: 0.3200 (mmtt) REVERT: Lz 144 MET cc_start: 0.1079 (mtt) cc_final: -0.0036 (mmt) outliers start: 320 outliers final: 146 residues processed: 1524 average time/residue: 2.0721 time to fit residues: 4536.8674 Evaluate side-chains 1435 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1270 time to evaluate : 6.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 4 VAL Chi-restraints excluded: chain LA residue 15 VAL Chi-restraints excluded: chain LA residue 75 LEU Chi-restraints excluded: chain LA residue 102 LEU Chi-restraints excluded: chain LA residue 135 THR Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LA residue 208 GLU Chi-restraints excluded: chain LB residue 17 LEU Chi-restraints excluded: chain LB residue 70 LYS Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 266 VAL Chi-restraints excluded: chain LB residue 305 THR Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LB residue 351 LEU Chi-restraints excluded: chain LB residue 360 LEU Chi-restraints excluded: chain LB residue 395 ASP Chi-restraints excluded: chain LC residue 8 ILE Chi-restraints excluded: chain LC residue 22 VAL Chi-restraints excluded: chain LC residue 87 SER Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 319 LEU Chi-restraints excluded: chain LC residue 334 THR Chi-restraints excluded: chain LC residue 349 LEU Chi-restraints excluded: chain LC residue 351 VAL Chi-restraints excluded: chain LD residue 46 THR Chi-restraints excluded: chain LD residue 194 VAL Chi-restraints excluded: chain LD residue 227 ILE Chi-restraints excluded: chain LD residue 232 THR Chi-restraints excluded: chain LD residue 236 MET Chi-restraints excluded: chain LD residue 271 MET Chi-restraints excluded: chain LE residue 88 VAL Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LF residue 123 VAL Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 156 VAL Chi-restraints excluded: chain LG residue 192 ARG Chi-restraints excluded: chain LG residue 233 ILE Chi-restraints excluded: chain LG residue 261 LEU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 58 ASP Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 79 SER Chi-restraints excluded: chain LI residue 89 VAL Chi-restraints excluded: chain LJ residue 26 VAL Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 133 VAL Chi-restraints excluded: chain LL residue 64 VAL Chi-restraints excluded: chain LL residue 109 SER Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LM residue 31 ILE Chi-restraints excluded: chain LM residue 33 GLN Chi-restraints excluded: chain LM residue 38 VAL Chi-restraints excluded: chain LM residue 70 GLN Chi-restraints excluded: chain LM residue 125 ASN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 145 ASN Chi-restraints excluded: chain LN residue 153 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 164 LEU Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 64 THR Chi-restraints excluded: chain LO residue 78 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 141 LEU Chi-restraints excluded: chain LO residue 193 THR Chi-restraints excluded: chain LP residue 36 ILE Chi-restraints excluded: chain LP residue 85 LYS Chi-restraints excluded: chain LP residue 129 THR Chi-restraints excluded: chain LQ residue 19 LYS Chi-restraints excluded: chain LQ residue 79 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 114 LEU Chi-restraints excluded: chain LQ residue 128 LEU Chi-restraints excluded: chain LR residue 13 SER Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LS residue 16 CYS Chi-restraints excluded: chain LS residue 69 GLU Chi-restraints excluded: chain LS residue 80 ILE Chi-restraints excluded: chain LS residue 85 ASP Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LT residue 29 THR Chi-restraints excluded: chain LT residue 120 LYS Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 45 GLU Chi-restraints excluded: chain LU residue 102 VAL Chi-restraints excluded: chain LV residue 18 LEU Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 65 VAL Chi-restraints excluded: chain LV residue 94 VAL Chi-restraints excluded: chain LV residue 112 MET Chi-restraints excluded: chain LV residue 118 THR Chi-restraints excluded: chain LW residue 1 MET Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 53 VAL Chi-restraints excluded: chain LW residue 54 LEU Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 91 ASN Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LZ residue 11 VAL Chi-restraints excluded: chain LZ residue 95 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain La residue 132 ARG Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lc residue 45 LEU Chi-restraints excluded: chain Lc residue 48 LEU Chi-restraints excluded: chain Lc residue 91 VAL Chi-restraints excluded: chain Lc residue 104 ILE Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 33 ILE Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 84 ILE Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Le residue 13 VAL Chi-restraints excluded: chain Le residue 34 ASN Chi-restraints excluded: chain Le residue 45 VAL Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Le residue 92 ASN Chi-restraints excluded: chain Le residue 94 SER Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 76 ARG Chi-restraints excluded: chain Lf residue 83 MET Chi-restraints excluded: chain Lg residue 2 VAL Chi-restraints excluded: chain Lg residue 22 LEU Chi-restraints excluded: chain Lh residue 29 SER Chi-restraints excluded: chain Lh residue 36 VAL Chi-restraints excluded: chain Lh residue 87 LYS Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Li residue 18 THR Chi-restraints excluded: chain Lj residue 10 LYS Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ll residue 35 ILE Chi-restraints excluded: chain Ln residue 10 MET Chi-restraints excluded: chain Lo residue 4 VAL Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 22 LYS Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lp residue 8 VAL Chi-restraints excluded: chain Lp residue 26 VAL Chi-restraints excluded: chain Lp residue 45 THR Chi-restraints excluded: chain Lp residue 63 THR Chi-restraints excluded: chain Lr residue 21 ASN Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 47 LYS Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 51 VAL Chi-restraints excluded: chain Lr residue 60 VAL Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 111 ILE Chi-restraints excluded: chain Lz residue 128 LEU Chi-restraints excluded: chain Lz residue 148 VAL Chi-restraints excluded: chain Lz residue 172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 954 optimal weight: 2.9990 chunk 726 optimal weight: 2.9990 chunk 501 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 461 optimal weight: 2.9990 chunk 648 optimal weight: 4.9990 chunk 969 optimal weight: 5.9990 chunk 1026 optimal weight: 0.9990 chunk 506 optimal weight: 0.9990 chunk 918 optimal weight: 0.9980 chunk 276 optimal weight: 80.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 132 ASN ** LA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 289 GLN LE 250 GLN LE 256 GLN LE 268 GLN LF 63 GLN LG 46 GLN LG 141 ASN LG 159 HIS ** LH 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 78 GLN LI 133 GLN LI 177 ASN LJ 98 ASN LJ 104 ASN LJ 167 GLN LM 78 GLN LN 199 GLN LS 125 GLN LU 95 ASN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 14 ASN LY 43 ASN LZ 78 ASN La 85 GLN La 120 GLN ** Lb 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lb 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lc 40 GLN Lh 20 GLN Lh 30 GLN Lh 65 GLN Lh 68 ASN Lh 108 GLN Li 36 HIS Ll 19 GLN Lm 120 ASN Lr 100 ASN Lr 121 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 151875 Z= 0.193 Angle : 0.612 25.308 224442 Z= 0.309 Chirality : 0.041 2.578 28025 Planarity : 0.005 0.107 13439 Dihedral : 24.586 179.900 71464 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.30 % Favored : 93.58 % Rotamer: Outliers : 3.84 % Allowed : 22.56 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.17 % Twisted Proline : 1.77 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.10), residues: 6696 helix: 0.96 (0.11), residues: 2418 sheet: -1.06 (0.16), residues: 923 loop : -1.42 (0.10), residues: 3355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPLN 120 HIS 0.012 0.001 HISLE 128 PHE 0.029 0.001 PHELD 3 TYR 0.021 0.002 TYRLT 65 ARG 0.011 0.000 ARGLZ 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1590 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1369 time to evaluate : 6.672 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: LA 141 PRO cc_start: 0.8706 (Cg_endo) cc_final: 0.8073 (Cg_exo) REVERT: LB 17 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7450 (pt) REVERT: LB 167 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: LB 216 MET cc_start: 0.8142 (mmm) cc_final: 0.7851 (mmt) REVERT: LB 348 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8137 (ptt90) REVERT: LB 351 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7914 (pp) REVERT: LC 268 ARG cc_start: 0.7717 (mtp-110) cc_final: 0.7455 (mtp-110) REVERT: LD 86 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.6034 (p90) REVERT: LE 62 MET cc_start: 0.8827 (mmm) cc_final: 0.8402 (mmt) REVERT: LF 33 LEU cc_start: 0.8886 (tt) cc_final: 0.8686 (tp) REVERT: LG 43 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7640 (mt0) REVERT: LH 142 ASP cc_start: 0.7516 (p0) cc_final: 0.7273 (p0) REVERT: LI 213 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6843 (t70) REVERT: LL 129 ARG cc_start: 0.7640 (mmm160) cc_final: 0.7378 (mmm-85) REVERT: LM 50 MET cc_start: 0.7718 (ttm) cc_final: 0.7450 (ttm) REVERT: LN 5 LYS cc_start: 0.8545 (tttp) cc_final: 0.8337 (tttt) REVERT: LN 153 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8508 (mptt) REVERT: LN 204 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.6324 (mtt90) REVERT: LO 78 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7894 (mmt180) REVERT: LO 180 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: LP 99 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: LQ 128 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8807 (mm) REVERT: LR 28 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7041 (mm-30) REVERT: LR 31 GLU cc_start: 0.7394 (pm20) cc_final: 0.7182 (pm20) REVERT: LS 80 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8943 (mm) REVERT: LT 104 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.8106 (p) REVERT: LU 40 GLU cc_start: 0.7637 (tm-30) cc_final: 0.6363 (tm-30) REVERT: LU 41 GLN cc_start: 0.7887 (pt0) cc_final: 0.7599 (pp30) REVERT: LW 1 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6367 (tmm) REVERT: LW 30 GLN cc_start: 0.8199 (mp-120) cc_final: 0.7904 (mm-40) REVERT: LW 50 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8695 (m-40) REVERT: LY 65 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: La 106 SER cc_start: 0.8681 (m) cc_final: 0.8317 (m) REVERT: Lb 65 MET cc_start: 0.7471 (mmp) cc_final: 0.7249 (mpp) REVERT: Lc 61 GLU cc_start: 0.7077 (tp30) cc_final: 0.6750 (tp30) REVERT: Le 55 MET cc_start: 0.8734 (mtm) cc_final: 0.8484 (mtm) REVERT: Lh 111 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: Lm 94 MET cc_start: 0.8252 (mmm) cc_final: 0.7989 (mmm) REVERT: Ln 11 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7254 (tpt-90) REVERT: Ln 17 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8662 (mtt180) REVERT: Ln 21 ARG cc_start: 0.8889 (mtp180) cc_final: 0.6903 (tpt170) REVERT: Lp 33 GLN cc_start: 0.8478 (tt0) cc_final: 0.8120 (tt0) REVERT: Lz 78 LYS cc_start: 0.4317 (mmpt) cc_final: 0.3640 (mmtt) REVERT: Lz 144 MET cc_start: 0.1057 (mtt) cc_final: -0.0050 (mmt) outliers start: 221 outliers final: 94 residues processed: 1488 average time/residue: 2.1356 time to fit residues: 4568.2351 Evaluate side-chains 1387 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1274 time to evaluate : 6.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 4 VAL Chi-restraints excluded: chain LA residue 15 VAL Chi-restraints excluded: chain LA residue 75 LEU Chi-restraints excluded: chain LA residue 102 LEU Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 17 LEU Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 135 LYS Chi-restraints excluded: chain LB residue 167 GLN Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LB residue 348 ARG Chi-restraints excluded: chain LB residue 351 LEU Chi-restraints excluded: chain LB residue 363 ILE Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 261 ASP Chi-restraints excluded: chain LC residue 334 THR Chi-restraints excluded: chain LD residue 86 TYR Chi-restraints excluded: chain LD residue 194 VAL Chi-restraints excluded: chain LD residue 232 THR Chi-restraints excluded: chain LE residue 88 VAL Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LF residue 213 LEU Chi-restraints excluded: chain LG residue 43 GLN Chi-restraints excluded: chain LG residue 156 VAL Chi-restraints excluded: chain LG residue 261 LEU Chi-restraints excluded: chain LI residue 35 ASP Chi-restraints excluded: chain LI residue 43 VAL Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 71 CYS Chi-restraints excluded: chain LI residue 133 GLN Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 213 HIS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 133 VAL Chi-restraints excluded: chain LL residue 109 SER Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 38 VAL Chi-restraints excluded: chain LM residue 70 GLN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 145 ASN Chi-restraints excluded: chain LN residue 153 LYS Chi-restraints excluded: chain LN residue 164 LEU Chi-restraints excluded: chain LN residue 204 ARG Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 64 THR Chi-restraints excluded: chain LO residue 78 ARG Chi-restraints excluded: chain LO residue 141 LEU Chi-restraints excluded: chain LO residue 180 GLN Chi-restraints excluded: chain LP residue 85 LYS Chi-restraints excluded: chain LP residue 99 GLU Chi-restraints excluded: chain LQ residue 19 LYS Chi-restraints excluded: chain LQ residue 79 THR Chi-restraints excluded: chain LQ residue 114 LEU Chi-restraints excluded: chain LQ residue 128 LEU Chi-restraints excluded: chain LR residue 119 MET Chi-restraints excluded: chain LS residue 16 CYS Chi-restraints excluded: chain LS residue 80 ILE Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LT residue 29 THR Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LV residue 65 VAL Chi-restraints excluded: chain LV residue 118 THR Chi-restraints excluded: chain LW residue 1 MET Chi-restraints excluded: chain LW residue 50 ASN Chi-restraints excluded: chain LW residue 54 LEU Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 31 SER Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 58 VAL Chi-restraints excluded: chain LY residue 65 GLN Chi-restraints excluded: chain LZ residue 11 VAL Chi-restraints excluded: chain LZ residue 88 ASP Chi-restraints excluded: chain LZ residue 95 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lc residue 15 ASN Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 100 ASN Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Le residue 34 ASN Chi-restraints excluded: chain Le residue 45 VAL Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Le residue 94 SER Chi-restraints excluded: chain Le residue 129 LEU Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 76 ARG Chi-restraints excluded: chain Lg residue 2 VAL Chi-restraints excluded: chain Lg residue 86 CYS Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 111 GLU Chi-restraints excluded: chain Li residue 32 ARG Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lp residue 63 THR Chi-restraints excluded: chain Lr residue 21 ASN Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 101 LYS Chi-restraints excluded: chain Lz residue 148 VAL Chi-restraints excluded: chain Lz residue 172 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 854 optimal weight: 4.9990 chunk 582 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 764 optimal weight: 2.9990 chunk 423 optimal weight: 1.9990 chunk 875 optimal weight: 6.9990 chunk 709 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 524 optimal weight: 0.7980 chunk 921 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 132 ASN LA 162 ASN LB 289 GLN LC 61 GLN LC 119 GLN LD 191 ASN ** LE 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 250 GLN LE 256 GLN LF 63 GLN LG 46 GLN LG 159 HIS ** LH 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 78 GLN LH 163 GLN LI 133 GLN LI 177 ASN LJ 98 ASN LM 78 GLN LN 199 GLN LP 40 HIS LP 118 GLN LS 125 GLN LU 95 ASN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 20 ASN LZ 78 ASN La 85 GLN La 120 GLN Lb 19 ASN ** Lb 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lc 33 GLN Lc 40 GLN Lh 20 GLN Lh 65 GLN Lh 68 ASN Lh 107 GLN Lh 108 GLN Li 36 HIS Lm 120 ASN Lr 30 ASN Lr 100 ASN Lr 121 GLN ** Lz 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 151875 Z= 0.281 Angle : 0.640 24.957 224442 Z= 0.324 Chirality : 0.043 2.574 28025 Planarity : 0.005 0.103 13439 Dihedral : 24.521 179.600 71461 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.60 % Favored : 93.29 % Rotamer: Outliers : 4.56 % Allowed : 23.58 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.17 % Twisted Proline : 1.77 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.10), residues: 6696 helix: 1.05 (0.11), residues: 2431 sheet: -0.94 (0.16), residues: 889 loop : -1.32 (0.10), residues: 3376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPLC 67 HIS 0.014 0.001 HISLE 128 PHE 0.022 0.002 PHELD 3 TYR 0.025 0.002 TYRLT 65 ARG 0.013 0.001 ARGLZ 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1305 time to evaluate : 6.843 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: LB 167 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8241 (mt0) REVERT: LB 348 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8135 (ptt90) REVERT: LB 351 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7924 (pp) REVERT: LC 268 ARG cc_start: 0.7663 (mtp-110) cc_final: 0.7415 (mtp-110) REVERT: LD 86 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6106 (p90) REVERT: LE 62 MET cc_start: 0.8903 (mmm) cc_final: 0.8453 (mmt) REVERT: LG 43 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: LH 142 ASP cc_start: 0.7465 (p0) cc_final: 0.7186 (p0) REVERT: LJ 60 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6709 (p90) REVERT: LL 129 ARG cc_start: 0.7694 (mmm160) cc_final: 0.7398 (mmm160) REVERT: LM 33 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6835 (tp40) REVERT: LM 50 MET cc_start: 0.7777 (ttm) cc_final: 0.7495 (ttm) REVERT: LN 153 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8650 (mptt) REVERT: LN 204 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6399 (mtt90) REVERT: LO 78 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7906 (mmt180) REVERT: LO 144 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: LO 180 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: LS 80 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8971 (mm) REVERT: LU 19 LEU cc_start: 0.8187 (mt) cc_final: 0.7450 (mp) REVERT: LV 112 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8021 (mtm) REVERT: LW 1 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6360 (tmm) REVERT: LW 50 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8742 (m-40) REVERT: La 106 SER cc_start: 0.8730 (m) cc_final: 0.8373 (m) REVERT: La 134 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: Lb 22 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7381 (mmmm) REVERT: Lb 65 MET cc_start: 0.7580 (mmp) cc_final: 0.7375 (mpp) REVERT: Lc 61 GLU cc_start: 0.7038 (tp30) cc_final: 0.6691 (tp30) REVERT: Ld 64 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9291 (mm) REVERT: Lh 7 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7363 (mpp80) REVERT: Lh 107 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: Lh 111 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: Ll 35 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8633 (mt) REVERT: Ll 36 ARG cc_start: 0.7938 (mtt-85) cc_final: 0.7712 (mtt-85) REVERT: Lm 94 MET cc_start: 0.8269 (mmm) cc_final: 0.8065 (mmm) REVERT: Ln 11 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7248 (tpt-90) REVERT: Ln 21 ARG cc_start: 0.8902 (mtp180) cc_final: 0.6947 (tpt170) REVERT: Lp 10 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8872 (tp) REVERT: Lp 33 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: Lz 78 LYS cc_start: 0.4324 (mmpt) cc_final: 0.3631 (mmtt) REVERT: Lz 144 MET cc_start: 0.1006 (mtt) cc_final: -0.0121 (mmt) outliers start: 262 outliers final: 129 residues processed: 1439 average time/residue: 2.0591 time to fit residues: 4269.3647 Evaluate side-chains 1431 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1277 time to evaluate : 6.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 4 VAL Chi-restraints excluded: chain LA residue 15 VAL Chi-restraints excluded: chain LA residue 75 LEU Chi-restraints excluded: chain LA residue 102 LEU Chi-restraints excluded: chain LA residue 154 SER Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 135 LYS Chi-restraints excluded: chain LB residue 167 GLN Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 305 THR Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LB residue 348 ARG Chi-restraints excluded: chain LB residue 351 LEU Chi-restraints excluded: chain LB residue 363 ILE Chi-restraints excluded: chain LB residue 395 ASP Chi-restraints excluded: chain LC residue 8 ILE Chi-restraints excluded: chain LC residue 87 SER Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 261 ASP Chi-restraints excluded: chain LC residue 312 ARG Chi-restraints excluded: chain LC residue 319 LEU Chi-restraints excluded: chain LC residue 351 VAL Chi-restraints excluded: chain LD residue 86 TYR Chi-restraints excluded: chain LD residue 194 VAL Chi-restraints excluded: chain LD residue 232 THR Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LF residue 213 LEU Chi-restraints excluded: chain LG residue 43 GLN Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 156 VAL Chi-restraints excluded: chain LG residue 192 ARG Chi-restraints excluded: chain LG residue 261 LEU Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 71 CYS Chi-restraints excluded: chain LI residue 102 MET Chi-restraints excluded: chain LI residue 123 GLN Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 60 PHE Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 133 VAL Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LL residue 64 VAL Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LM residue 31 ILE Chi-restraints excluded: chain LM residue 33 GLN Chi-restraints excluded: chain LM residue 38 VAL Chi-restraints excluded: chain LM residue 70 GLN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 145 ASN Chi-restraints excluded: chain LN residue 153 LYS Chi-restraints excluded: chain LN residue 164 LEU Chi-restraints excluded: chain LN residue 204 ARG Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 64 THR Chi-restraints excluded: chain LO residue 78 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 141 LEU Chi-restraints excluded: chain LO residue 144 GLU Chi-restraints excluded: chain LO residue 180 GLN Chi-restraints excluded: chain LP residue 36 ILE Chi-restraints excluded: chain LP residue 57 CYS Chi-restraints excluded: chain LP residue 85 LYS Chi-restraints excluded: chain LP residue 110 ASP Chi-restraints excluded: chain LP residue 118 GLN Chi-restraints excluded: chain LP residue 129 THR Chi-restraints excluded: chain LQ residue 19 LYS Chi-restraints excluded: chain LQ residue 79 THR Chi-restraints excluded: chain LQ residue 114 LEU Chi-restraints excluded: chain LR residue 13 SER Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LS residue 16 CYS Chi-restraints excluded: chain LS residue 80 ILE Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LT residue 29 THR Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LU residue 22 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 65 VAL Chi-restraints excluded: chain LV residue 94 VAL Chi-restraints excluded: chain LV residue 112 MET Chi-restraints excluded: chain LV residue 118 THR Chi-restraints excluded: chain LW residue 1 MET Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 50 ASN Chi-restraints excluded: chain LW residue 54 LEU Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 58 VAL Chi-restraints excluded: chain LY residue 91 ASN Chi-restraints excluded: chain LZ residue 11 VAL Chi-restraints excluded: chain LZ residue 95 VAL Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain La residue 63 LEU Chi-restraints excluded: chain La residue 132 ARG Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lb residue 22 LYS Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lc residue 65 MET Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 64 ILE Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain Ld residue 121 ASN Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Le residue 34 ASN Chi-restraints excluded: chain Le residue 45 VAL Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Le residue 94 SER Chi-restraints excluded: chain Le residue 129 LEU Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 76 ARG Chi-restraints excluded: chain Lf residue 83 MET Chi-restraints excluded: chain Lg residue 2 VAL Chi-restraints excluded: chain Lg residue 48 VAL Chi-restraints excluded: chain Lg residue 86 CYS Chi-restraints excluded: chain Lh residue 7 ARG Chi-restraints excluded: chain Lh residue 29 SER Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 107 GLN Chi-restraints excluded: chain Lh residue 111 GLU Chi-restraints excluded: chain Li residue 32 ARG Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ll residue 35 ILE Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lp residue 10 ILE Chi-restraints excluded: chain Lp residue 33 GLN Chi-restraints excluded: chain Lp residue 63 THR Chi-restraints excluded: chain Lr residue 21 ASN Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 51 VAL Chi-restraints excluded: chain Lr residue 60 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 148 VAL Chi-restraints excluded: chain Lz residue 172 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 345 optimal weight: 6.9990 chunk 924 optimal weight: 0.7980 chunk 202 optimal weight: 30.0000 chunk 602 optimal weight: 3.9990 chunk 253 optimal weight: 8.9990 chunk 1027 optimal weight: 7.9990 chunk 852 optimal weight: 5.9990 chunk 475 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 339 optimal weight: 10.0000 chunk 539 optimal weight: 0.0980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 132 ASN LB 289 GLN ** LE 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 250 GLN LE 256 GLN LF 63 GLN LG 46 GLN LG 159 HIS LG 208 ASN LH 39 ASN LH 78 GLN LI 133 GLN LI 177 ASN LI 213 HIS LJ 98 ASN ** LM 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 199 GLN LU 95 ASN LW 48 GLN LZ 78 ASN La 85 GLN Lb 19 ASN Lb 60 ASN Lb 61 ASN Lc 40 GLN Lh 20 GLN Lh 30 GLN Lh 65 GLN Lh 68 ASN Lh 98 HIS Li 36 HIS Lm 90 ASN Lm 120 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 151875 Z= 0.291 Angle : 0.640 24.857 224442 Z= 0.324 Chirality : 0.043 2.577 28025 Planarity : 0.005 0.098 13439 Dihedral : 24.500 179.933 71461 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.85 % Favored : 93.04 % Rotamer: Outliers : 4.54 % Allowed : 24.07 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.17 % Twisted Proline : 1.77 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.10), residues: 6696 helix: 1.13 (0.11), residues: 2423 sheet: -0.94 (0.16), residues: 899 loop : -1.28 (0.10), residues: 3374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPLC 67 HIS 0.013 0.001 HISLE 128 PHE 0.020 0.002 PHELD 3 TYR 0.026 0.002 TYRLT 65 ARG 0.016 0.001 ARGLZ 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1576 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1315 time to evaluate : 6.849 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: LA 3 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8376 (ptp-170) REVERT: LA 208 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: LB 17 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6797 (pt) REVERT: LB 167 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: LB 348 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8162 (ptt90) REVERT: LB 351 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7905 (pp) REVERT: LC 268 ARG cc_start: 0.7635 (mtp-110) cc_final: 0.7410 (mtp-110) REVERT: LD 115 MET cc_start: 0.8296 (ptp) cc_final: 0.7973 (ptm) REVERT: LE 245 GLN cc_start: 0.8290 (tp40) cc_final: 0.7688 (tp-100) REVERT: LG 43 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7601 (mt0) REVERT: LG 176 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8192 (ttmt) REVERT: LG 229 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7470 (ppp80) REVERT: LH 142 ASP cc_start: 0.7494 (p0) cc_final: 0.7202 (p0) REVERT: LL 129 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7550 (mmm-85) REVERT: LM 50 MET cc_start: 0.7734 (ttm) cc_final: 0.7427 (ttm) REVERT: LN 153 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8631 (mptt) REVERT: LN 204 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6332 (mtt90) REVERT: LO 78 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7926 (mmt180) REVERT: LO 144 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: LS 80 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8953 (mm) REVERT: LU 19 LEU cc_start: 0.8209 (mt) cc_final: 0.7508 (mp) REVERT: LV 112 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8029 (mtm) REVERT: LV 124 GLU cc_start: 0.8372 (mp0) cc_final: 0.8156 (mp0) REVERT: LW 1 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6388 (tmm) REVERT: LW 30 GLN cc_start: 0.8146 (mp-120) cc_final: 0.7932 (mm-40) REVERT: LW 50 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8734 (m-40) REVERT: LY 8 THR cc_start: 0.8886 (t) cc_final: 0.8535 (t) REVERT: LY 65 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: La 77 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8218 (mmtt) REVERT: La 106 SER cc_start: 0.8726 (m) cc_final: 0.8378 (m) REVERT: Lb 22 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7394 (mmmm) REVERT: Lc 61 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: Ld 64 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9302 (mm) REVERT: Lg 89 ASP cc_start: 0.7412 (m-30) cc_final: 0.7127 (m-30) REVERT: Lg 100 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: Lh 7 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7642 (mpp80) REVERT: Lh 111 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: Lk 17 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8496 (ttp-170) REVERT: Ln 1 MET cc_start: 0.4639 (OUTLIER) cc_final: 0.4409 (mmt) REVERT: Ln 11 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7265 (tpt-90) REVERT: Ln 17 ARG cc_start: 0.8928 (mtm-85) cc_final: 0.8674 (mtt180) REVERT: Ln 21 ARG cc_start: 0.8907 (mtp180) cc_final: 0.6949 (tpt170) REVERT: Ln 23 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7501 (ptm-80) REVERT: Lp 10 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8860 (tp) REVERT: Lp 33 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: Lz 78 LYS cc_start: 0.4313 (mmpt) cc_final: 0.3654 (mmtt) REVERT: Lz 144 MET cc_start: 0.1210 (mtt) cc_final: 0.0077 (mmt) outliers start: 261 outliers final: 151 residues processed: 1454 average time/residue: 2.1141 time to fit residues: 4412.2953 Evaluate side-chains 1457 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1276 time to evaluate : 6.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 3 ARG Chi-restraints excluded: chain LA residue 4 VAL Chi-restraints excluded: chain LA residue 15 VAL Chi-restraints excluded: chain LA residue 75 LEU Chi-restraints excluded: chain LA residue 102 LEU Chi-restraints excluded: chain LA residue 154 SER Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LA residue 208 GLU Chi-restraints excluded: chain LB residue 17 LEU Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 135 LYS Chi-restraints excluded: chain LB residue 167 GLN Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 298 LEU Chi-restraints excluded: chain LB residue 305 THR Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LB residue 348 ARG Chi-restraints excluded: chain LB residue 351 LEU Chi-restraints excluded: chain LB residue 363 ILE Chi-restraints excluded: chain LB residue 395 ASP Chi-restraints excluded: chain LC residue 8 ILE Chi-restraints excluded: chain LC residue 22 VAL Chi-restraints excluded: chain LC residue 87 SER Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 261 ASP Chi-restraints excluded: chain LC residue 319 LEU Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LD residue 194 VAL Chi-restraints excluded: chain LD residue 227 ILE Chi-restraints excluded: chain LD residue 232 THR Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LF residue 213 LEU Chi-restraints excluded: chain LG residue 43 GLN Chi-restraints excluded: chain LG residue 156 VAL Chi-restraints excluded: chain LG residue 176 LYS Chi-restraints excluded: chain LG residue 184 ILE Chi-restraints excluded: chain LG residue 192 ARG Chi-restraints excluded: chain LG residue 229 ARG Chi-restraints excluded: chain LG residue 261 LEU Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 71 CYS Chi-restraints excluded: chain LI residue 102 MET Chi-restraints excluded: chain LI residue 123 GLN Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 133 VAL Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LL residue 64 VAL Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LM residue 31 ILE Chi-restraints excluded: chain LM residue 38 VAL Chi-restraints excluded: chain LM residue 70 GLN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 38 ARG Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 149 GLN Chi-restraints excluded: chain LN residue 153 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 164 LEU Chi-restraints excluded: chain LN residue 204 ARG Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 64 THR Chi-restraints excluded: chain LO residue 78 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 141 LEU Chi-restraints excluded: chain LO residue 144 GLU Chi-restraints excluded: chain LP residue 36 ILE Chi-restraints excluded: chain LP residue 57 CYS Chi-restraints excluded: chain LP residue 76 TRP Chi-restraints excluded: chain LP residue 85 LYS Chi-restraints excluded: chain LP residue 110 ASP Chi-restraints excluded: chain LP residue 129 THR Chi-restraints excluded: chain LQ residue 19 LYS Chi-restraints excluded: chain LQ residue 79 THR Chi-restraints excluded: chain LQ residue 114 LEU Chi-restraints excluded: chain LR residue 13 SER Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LS residue 16 CYS Chi-restraints excluded: chain LS residue 80 ILE Chi-restraints excluded: chain LS residue 85 ASP Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LT residue 29 THR Chi-restraints excluded: chain LT residue 84 ILE Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LU residue 22 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 65 VAL Chi-restraints excluded: chain LV residue 94 VAL Chi-restraints excluded: chain LV residue 112 MET Chi-restraints excluded: chain LV residue 118 THR Chi-restraints excluded: chain LW residue 1 MET Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 50 ASN Chi-restraints excluded: chain LW residue 54 LEU Chi-restraints excluded: chain LX residue 40 ILE Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 58 VAL Chi-restraints excluded: chain LY residue 65 GLN Chi-restraints excluded: chain LY residue 91 ASN Chi-restraints excluded: chain LZ residue 11 VAL Chi-restraints excluded: chain LZ residue 88 ASP Chi-restraints excluded: chain LZ residue 95 VAL Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain La residue 63 LEU Chi-restraints excluded: chain La residue 77 LYS Chi-restraints excluded: chain La residue 116 LYS Chi-restraints excluded: chain La residue 132 ARG Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lb residue 22 LYS Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lc residue 45 LEU Chi-restraints excluded: chain Lc residue 48 LEU Chi-restraints excluded: chain Lc residue 61 GLU Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 64 ILE Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain Ld residue 121 ASN Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Le residue 34 ASN Chi-restraints excluded: chain Le residue 45 VAL Chi-restraints excluded: chain Le residue 53 ILE Chi-restraints excluded: chain Le residue 83 LYS Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Le residue 94 SER Chi-restraints excluded: chain Le residue 129 LEU Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 76 ARG Chi-restraints excluded: chain Lf residue 83 MET Chi-restraints excluded: chain Lg residue 2 VAL Chi-restraints excluded: chain Lg residue 22 LEU Chi-restraints excluded: chain Lg residue 48 VAL Chi-restraints excluded: chain Lg residue 86 CYS Chi-restraints excluded: chain Lg residue 100 GLN Chi-restraints excluded: chain Lh residue 7 ARG Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 29 SER Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 110 LYS Chi-restraints excluded: chain Lh residue 111 GLU Chi-restraints excluded: chain Li residue 32 ARG Chi-restraints excluded: chain Li residue 64 SER Chi-restraints excluded: chain Lk residue 17 ARG Chi-restraints excluded: chain Ln residue 1 MET Chi-restraints excluded: chain Ln residue 23 ARG Chi-restraints excluded: chain Lo residue 4 VAL Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 24 THR Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lp residue 10 ILE Chi-restraints excluded: chain Lp residue 33 GLN Chi-restraints excluded: chain Lp residue 45 THR Chi-restraints excluded: chain Lp residue 63 THR Chi-restraints excluded: chain Lr residue 21 ASN Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 51 VAL Chi-restraints excluded: chain Lr residue 60 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 101 LYS Chi-restraints excluded: chain Lz residue 148 VAL Chi-restraints excluded: chain Lz residue 172 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 990 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 585 optimal weight: 10.0000 chunk 750 optimal weight: 0.9990 chunk 581 optimal weight: 0.8980 chunk 864 optimal weight: 10.0000 chunk 573 optimal weight: 0.9980 chunk 1023 optimal weight: 7.9990 chunk 640 optimal weight: 20.0000 chunk 624 optimal weight: 4.9990 chunk 472 optimal weight: 0.0040 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 132 ASN LA 187 HIS LB 289 GLN LE 245 GLN LE 250 GLN LE 256 GLN LF 163 ASN LG 46 GLN LG 159 HIS LG 208 ASN LG 227 ASN LH 39 ASN LH 78 GLN LI 133 GLN LI 177 ASN LJ 98 ASN ** LM 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 199 GLN LO 180 GLN LO 184 ASN LQ 125 GLN LS 125 GLN LU 95 ASN LW 48 GLN LY 14 ASN LZ 78 ASN La 85 GLN La 120 GLN Lb 19 ASN Lb 61 ASN Lh 20 GLN Lh 65 GLN Lh 68 ASN Lh 108 GLN Li 36 HIS Lm 104 HIS Lm 120 ASN Lr 83 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 151875 Z= 0.190 Angle : 0.601 25.563 224442 Z= 0.304 Chirality : 0.040 2.553 28025 Planarity : 0.005 0.119 13439 Dihedral : 24.452 179.761 71461 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.75 % Favored : 93.13 % Rotamer: Outliers : 4.09 % Allowed : 25.06 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.17 % Twisted Proline : 1.77 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.10), residues: 6696 helix: 1.26 (0.11), residues: 2414 sheet: -0.94 (0.16), residues: 925 loop : -1.21 (0.10), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPLN 120 HIS 0.011 0.001 HISLE 128 PHE 0.023 0.001 PHELk 34 TYR 0.031 0.002 TYRLT 65 ARG 0.016 0.000 ARGLZ 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1554 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1319 time to evaluate : 6.863 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: LB 70 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8556 (mtpp) REVERT: LB 74 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: LB 167 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: LB 348 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8145 (ptt90) REVERT: LB 351 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7872 (pp) REVERT: LD 86 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.6394 (p90) REVERT: LD 115 MET cc_start: 0.8288 (ptp) cc_final: 0.7992 (ptm) REVERT: LE 245 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7710 (tp-100) REVERT: LG 43 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7590 (mt0) REVERT: LG 229 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7610 (ppp80) REVERT: LH 142 ASP cc_start: 0.7424 (p0) cc_final: 0.7120 (p0) REVERT: LM 50 MET cc_start: 0.7723 (ttm) cc_final: 0.7418 (ttm) REVERT: LN 153 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8554 (mptt) REVERT: LN 204 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6344 (mtt90) REVERT: LO 78 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7915 (mmt180) REVERT: LO 144 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: LP 99 GLU cc_start: 0.7269 (tt0) cc_final: 0.7031 (tt0) REVERT: LR 28 GLU cc_start: 0.7655 (mp0) cc_final: 0.7379 (mm-30) REVERT: LR 31 GLU cc_start: 0.7369 (pm20) cc_final: 0.6954 (pm20) REVERT: LS 80 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8915 (mm) REVERT: LT 104 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8184 (p) REVERT: LV 124 GLU cc_start: 0.8373 (mp0) cc_final: 0.8149 (mp0) REVERT: LW 1 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6478 (tmm) REVERT: LX 92 ASP cc_start: 0.7910 (m-30) cc_final: 0.7631 (m-30) REVERT: La 106 SER cc_start: 0.8672 (m) cc_final: 0.8348 (m) REVERT: Lb 19 ASN cc_start: 0.6906 (OUTLIER) cc_final: 0.6389 (m110) REVERT: Lb 22 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7335 (mmmm) REVERT: Lb 65 MET cc_start: 0.7268 (mmp) cc_final: 0.7018 (mpp) REVERT: Lc 61 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6647 (tp30) REVERT: Ld 64 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9304 (mm) REVERT: Le 55 MET cc_start: 0.8726 (mtm) cc_final: 0.8510 (mtm) REVERT: Lg 89 ASP cc_start: 0.7379 (m-30) cc_final: 0.7124 (m-30) REVERT: Lh 111 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: Lj 65 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.5974 (mtp180) REVERT: Ln 11 ARG cc_start: 0.7721 (mtt180) cc_final: 0.7244 (tpt-90) REVERT: Ln 17 ARG cc_start: 0.8899 (mtm-85) cc_final: 0.8698 (mtt180) REVERT: Ln 21 ARG cc_start: 0.8892 (mtp180) cc_final: 0.6966 (tpt170) REVERT: Ln 23 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7955 (ptm-80) REVERT: Lp 10 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8848 (tp) REVERT: Lp 33 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: Lp 63 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8878 (m) REVERT: Lz 78 LYS cc_start: 0.4286 (mmpt) cc_final: 0.3660 (mmtt) REVERT: Lz 144 MET cc_start: 0.1082 (mtt) cc_final: -0.0007 (mmt) outliers start: 235 outliers final: 122 residues processed: 1444 average time/residue: 2.0975 time to fit residues: 4369.4040 Evaluate side-chains 1422 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1274 time to evaluate : 6.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 4 VAL Chi-restraints excluded: chain LA residue 15 VAL Chi-restraints excluded: chain LA residue 75 LEU Chi-restraints excluded: chain LA residue 102 LEU Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 70 LYS Chi-restraints excluded: chain LB residue 74 GLU Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 135 LYS Chi-restraints excluded: chain LB residue 167 GLN Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 298 LEU Chi-restraints excluded: chain LB residue 305 THR Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LB residue 348 ARG Chi-restraints excluded: chain LB residue 351 LEU Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 261 ASP Chi-restraints excluded: chain LC residue 312 ARG Chi-restraints excluded: chain LC residue 319 LEU Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LD residue 86 TYR Chi-restraints excluded: chain LD residue 194 VAL Chi-restraints excluded: chain LD residue 232 THR Chi-restraints excluded: chain LE residue 245 GLN Chi-restraints excluded: chain LE residue 278 THR Chi-restraints excluded: chain LF residue 41 MET Chi-restraints excluded: chain LG residue 43 GLN Chi-restraints excluded: chain LG residue 156 VAL Chi-restraints excluded: chain LG residue 192 ARG Chi-restraints excluded: chain LG residue 229 ARG Chi-restraints excluded: chain LG residue 261 LEU Chi-restraints excluded: chain LI residue 71 CYS Chi-restraints excluded: chain LI residue 102 MET Chi-restraints excluded: chain LI residue 123 GLN Chi-restraints excluded: chain LI residue 133 GLN Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LM residue 31 ILE Chi-restraints excluded: chain LM residue 38 VAL Chi-restraints excluded: chain LM residue 70 GLN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 149 GLN Chi-restraints excluded: chain LN residue 153 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 164 LEU Chi-restraints excluded: chain LN residue 204 ARG Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 64 THR Chi-restraints excluded: chain LO residue 78 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 141 LEU Chi-restraints excluded: chain LO residue 144 GLU Chi-restraints excluded: chain LP residue 57 CYS Chi-restraints excluded: chain LP residue 85 LYS Chi-restraints excluded: chain LP residue 96 LYS Chi-restraints excluded: chain LQ residue 19 LYS Chi-restraints excluded: chain LQ residue 79 THR Chi-restraints excluded: chain LQ residue 114 LEU Chi-restraints excluded: chain LR residue 13 SER Chi-restraints excluded: chain LR residue 119 MET Chi-restraints excluded: chain LS residue 16 CYS Chi-restraints excluded: chain LS residue 80 ILE Chi-restraints excluded: chain LS residue 85 ASP Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LT residue 29 THR Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LU residue 22 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 65 VAL Chi-restraints excluded: chain LV residue 94 VAL Chi-restraints excluded: chain LV residue 118 THR Chi-restraints excluded: chain LW residue 1 MET Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 54 LEU Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 38 LEU Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 58 VAL Chi-restraints excluded: chain LY residue 91 ASN Chi-restraints excluded: chain LZ residue 11 VAL Chi-restraints excluded: chain LZ residue 88 ASP Chi-restraints excluded: chain LZ residue 95 VAL Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain La residue 63 LEU Chi-restraints excluded: chain La residue 132 ARG Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lb residue 19 ASN Chi-restraints excluded: chain Lb residue 22 LYS Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lc residue 14 ILE Chi-restraints excluded: chain Lc residue 45 LEU Chi-restraints excluded: chain Lc residue 61 GLU Chi-restraints excluded: chain Lc residue 65 MET Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 64 ILE Chi-restraints excluded: chain Ld residue 100 ASN Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain Ld residue 121 ASN Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Le residue 34 ASN Chi-restraints excluded: chain Le residue 45 VAL Chi-restraints excluded: chain Le residue 53 ILE Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Le residue 94 SER Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 76 ARG Chi-restraints excluded: chain Lg residue 2 VAL Chi-restraints excluded: chain Lg residue 22 LEU Chi-restraints excluded: chain Lg residue 86 CYS Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 29 SER Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 110 LYS Chi-restraints excluded: chain Lh residue 111 GLU Chi-restraints excluded: chain Li residue 32 ARG Chi-restraints excluded: chain Lj residue 65 ARG Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ln residue 23 ARG Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lp residue 10 ILE Chi-restraints excluded: chain Lp residue 33 GLN Chi-restraints excluded: chain Lp residue 63 THR Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 51 VAL Chi-restraints excluded: chain Lr residue 60 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 101 LYS Chi-restraints excluded: chain Lz residue 148 VAL Chi-restraints excluded: chain Lz residue 172 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 633 optimal weight: 4.9990 chunk 408 optimal weight: 10.0000 chunk 611 optimal weight: 4.9990 chunk 308 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 650 optimal weight: 3.9990 chunk 697 optimal weight: 3.9990 chunk 506 optimal weight: 0.2980 chunk 95 optimal weight: 7.9990 chunk 804 optimal weight: 2.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 132 ASN LA 139 HIS ** LB 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 256 GLN LF 63 GLN LF 163 ASN LG 46 GLN LG 159 HIS LG 208 ASN ** LH 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 78 GLN LI 177 ASN LI 213 HIS LJ 98 ASN LJ 167 GLN LL 40 GLN ** LM 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 180 GLN LQ 125 GLN ** LS 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 95 ASN LW 48 GLN LX 111 GLN LY 14 ASN LZ 78 ASN La 67 GLN La 85 GLN La 120 GLN Lb 61 ASN Ld 93 ASN Lh 65 GLN Lh 68 ASN Lh 108 GLN Li 36 HIS Lm 120 ASN Lr 121 GLN Lz 72 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 151875 Z= 0.318 Angle : 0.656 24.792 224442 Z= 0.332 Chirality : 0.044 2.580 28025 Planarity : 0.006 0.115 13439 Dihedral : 24.447 179.902 71461 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.82 % Favored : 93.07 % Rotamer: Outliers : 4.09 % Allowed : 25.29 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.17 % Twisted Proline : 1.77 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 6696 helix: 1.22 (0.11), residues: 2411 sheet: -0.93 (0.16), residues: 923 loop : -1.20 (0.10), residues: 3362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPLC 67 HIS 0.015 0.001 HISLE 128 PHE 0.027 0.002 PHELU 39 TYR 0.034 0.002 TYRLT 65 ARG 0.019 0.001 ARGLZ 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1280 time to evaluate : 6.867 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: LA 3 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8374 (ptp-170) REVERT: LA 208 GLU cc_start: 0.8040 (mp0) cc_final: 0.7769 (pm20) REVERT: LB 70 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8547 (mtpp) REVERT: LB 74 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: LB 167 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: LB 348 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8153 (ptt90) REVERT: LB 351 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7929 (pp) REVERT: LD 86 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6480 (p90) REVERT: LD 115 MET cc_start: 0.8343 (ptp) cc_final: 0.8020 (ptm) REVERT: LE 245 GLN cc_start: 0.8509 (tp40) cc_final: 0.7497 (tp-100) REVERT: LG 43 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7635 (mt0) REVERT: LG 176 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8204 (ttmt) REVERT: LG 229 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7613 (ppp80) REVERT: LH 142 ASP cc_start: 0.7458 (p0) cc_final: 0.7145 (p0) REVERT: LM 50 MET cc_start: 0.7798 (ttm) cc_final: 0.7480 (ttm) REVERT: LN 153 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8676 (mptt) REVERT: LN 204 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6398 (mtt90) REVERT: LO 78 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7914 (mmt180) REVERT: LO 144 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: LS 80 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8964 (mm) REVERT: LT 120 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7541 (tptm) REVERT: LW 1 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6373 (tmm) REVERT: LW 30 GLN cc_start: 0.8194 (mp-120) cc_final: 0.7877 (mm-40) REVERT: LY 65 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: La 106 SER cc_start: 0.8725 (m) cc_final: 0.8373 (m) REVERT: La 134 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: Lb 22 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7397 (mmmm) REVERT: Lb 27 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7627 (mm-40) REVERT: Lb 65 MET cc_start: 0.7329 (mmp) cc_final: 0.7128 (mpp) REVERT: Lc 61 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6762 (tp30) REVERT: Lg 89 ASP cc_start: 0.7428 (m-30) cc_final: 0.7188 (m-30) REVERT: Lh 23 ASP cc_start: 0.7731 (p0) cc_final: 0.7231 (p0) REVERT: Lh 111 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: Ln 11 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7333 (tpt-90) REVERT: Ln 17 ARG cc_start: 0.8956 (mtm-85) cc_final: 0.8719 (mtt180) REVERT: Ln 21 ARG cc_start: 0.8908 (mtp180) cc_final: 0.6964 (tpt170) REVERT: Ln 23 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7857 (ptm-80) REVERT: Lp 10 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8881 (tp) REVERT: Lp 33 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: Lz 78 LYS cc_start: 0.4207 (mmpt) cc_final: 0.3593 (mmtt) REVERT: Lz 144 MET cc_start: 0.1290 (mtt) cc_final: 0.0120 (mmt) outliers start: 235 outliers final: 145 residues processed: 1407 average time/residue: 2.1362 time to fit residues: 4330.8052 Evaluate side-chains 1424 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1253 time to evaluate : 6.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 3 ARG Chi-restraints excluded: chain LA residue 4 VAL Chi-restraints excluded: chain LA residue 15 VAL Chi-restraints excluded: chain LA residue 75 LEU Chi-restraints excluded: chain LA residue 102 LEU Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 17 LEU Chi-restraints excluded: chain LB residue 56 ILE Chi-restraints excluded: chain LB residue 70 LYS Chi-restraints excluded: chain LB residue 74 GLU Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 135 LYS Chi-restraints excluded: chain LB residue 162 VAL Chi-restraints excluded: chain LB residue 167 GLN Chi-restraints excluded: chain LB residue 194 LEU Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 298 LEU Chi-restraints excluded: chain LB residue 305 THR Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LB residue 348 ARG Chi-restraints excluded: chain LB residue 351 LEU Chi-restraints excluded: chain LB residue 363 ILE Chi-restraints excluded: chain LB residue 395 ASP Chi-restraints excluded: chain LC residue 14 LYS Chi-restraints excluded: chain LC residue 87 SER Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 319 LEU Chi-restraints excluded: chain LC residue 351 VAL Chi-restraints excluded: chain LD residue 86 TYR Chi-restraints excluded: chain LD residue 194 VAL Chi-restraints excluded: chain LD residue 227 ILE Chi-restraints excluded: chain LD residue 232 THR Chi-restraints excluded: chain LE residue 278 THR Chi-restraints excluded: chain LF residue 41 MET Chi-restraints excluded: chain LF residue 213 LEU Chi-restraints excluded: chain LG residue 28 VAL Chi-restraints excluded: chain LG residue 43 GLN Chi-restraints excluded: chain LG residue 156 VAL Chi-restraints excluded: chain LG residue 176 LYS Chi-restraints excluded: chain LG residue 192 ARG Chi-restraints excluded: chain LG residue 229 ARG Chi-restraints excluded: chain LG residue 252 LYS Chi-restraints excluded: chain LG residue 261 LEU Chi-restraints excluded: chain LI residue 71 CYS Chi-restraints excluded: chain LI residue 102 MET Chi-restraints excluded: chain LI residue 123 GLN Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 133 VAL Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LL residue 64 VAL Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 31 ILE Chi-restraints excluded: chain LM residue 38 VAL Chi-restraints excluded: chain LM residue 70 GLN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 149 GLN Chi-restraints excluded: chain LN residue 153 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 164 LEU Chi-restraints excluded: chain LN residue 204 ARG Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 64 THR Chi-restraints excluded: chain LO residue 78 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 141 LEU Chi-restraints excluded: chain LO residue 144 GLU Chi-restraints excluded: chain LP residue 36 ILE Chi-restraints excluded: chain LP residue 57 CYS Chi-restraints excluded: chain LP residue 76 TRP Chi-restraints excluded: chain LP residue 85 LYS Chi-restraints excluded: chain LP residue 96 LYS Chi-restraints excluded: chain LP residue 110 ASP Chi-restraints excluded: chain LP residue 129 THR Chi-restraints excluded: chain LQ residue 19 LYS Chi-restraints excluded: chain LQ residue 79 THR Chi-restraints excluded: chain LQ residue 114 LEU Chi-restraints excluded: chain LR residue 13 SER Chi-restraints excluded: chain LS residue 16 CYS Chi-restraints excluded: chain LS residue 80 ILE Chi-restraints excluded: chain LS residue 85 ASP Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LT residue 29 THR Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LT residue 120 LYS Chi-restraints excluded: chain LU residue 22 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LU residue 102 VAL Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 65 VAL Chi-restraints excluded: chain LV residue 94 VAL Chi-restraints excluded: chain LV residue 118 THR Chi-restraints excluded: chain LW residue 1 MET Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 54 LEU Chi-restraints excluded: chain LX residue 54 LEU Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 38 LEU Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 58 VAL Chi-restraints excluded: chain LY residue 65 GLN Chi-restraints excluded: chain LY residue 91 ASN Chi-restraints excluded: chain LZ residue 88 ASP Chi-restraints excluded: chain LZ residue 95 VAL Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain La residue 63 LEU Chi-restraints excluded: chain La residue 132 ARG Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lb residue 22 LYS Chi-restraints excluded: chain Lb residue 27 GLN Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lc residue 45 LEU Chi-restraints excluded: chain Lc residue 61 GLU Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 100 ASN Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain Ld residue 121 ASN Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Le residue 34 ASN Chi-restraints excluded: chain Le residue 45 VAL Chi-restraints excluded: chain Le residue 53 ILE Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Le residue 94 SER Chi-restraints excluded: chain Le residue 129 LEU Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 76 ARG Chi-restraints excluded: chain Lf residue 83 MET Chi-restraints excluded: chain Lg residue 2 VAL Chi-restraints excluded: chain Lg residue 22 LEU Chi-restraints excluded: chain Lg residue 48 VAL Chi-restraints excluded: chain Lg residue 86 CYS Chi-restraints excluded: chain Lh residue 29 SER Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 110 LYS Chi-restraints excluded: chain Lh residue 111 GLU Chi-restraints excluded: chain Li residue 18 THR Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ln residue 23 ARG Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lp residue 10 ILE Chi-restraints excluded: chain Lp residue 33 GLN Chi-restraints excluded: chain Lp residue 63 THR Chi-restraints excluded: chain Lr residue 14 SER Chi-restraints excluded: chain Lr residue 21 ASN Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 51 VAL Chi-restraints excluded: chain Lr residue 60 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 101 LYS Chi-restraints excluded: chain Lz residue 148 VAL Chi-restraints excluded: chain Lz residue 172 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 931 optimal weight: 4.9990 chunk 980 optimal weight: 5.9990 chunk 894 optimal weight: 2.9990 chunk 953 optimal weight: 5.9990 chunk 574 optimal weight: 0.9990 chunk 415 optimal weight: 0.9980 chunk 749 optimal weight: 0.8980 chunk 292 optimal weight: 50.0000 chunk 861 optimal weight: 2.9990 chunk 902 optimal weight: 0.9990 chunk 950 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 132 ASN ** LB 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 302 ASN LD 198 HIS LE 245 GLN LE 250 GLN LE 256 GLN LF 163 ASN LG 46 GLN LG 159 HIS LG 208 ASN ** LH 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 78 GLN LI 133 GLN LI 177 ASN LI 213 HIS ** LJ 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 78 GLN LO 180 GLN LO 184 ASN LQ 125 GLN LW 45 ASN LW 48 GLN LX 111 GLN LY 14 ASN LZ 78 ASN La 85 GLN La 120 GLN Lb 61 ASN Lh 65 GLN Lh 68 ASN Lm 120 ASN Lr 83 ASN Lz 72 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 151875 Z= 0.184 Angle : 0.613 25.763 224442 Z= 0.311 Chirality : 0.041 2.543 28025 Planarity : 0.005 0.107 13439 Dihedral : 24.456 179.853 71461 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.68 % Favored : 93.22 % Rotamer: Outliers : 3.30 % Allowed : 26.31 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.17 % Twisted Proline : 1.77 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.10), residues: 6696 helix: 1.29 (0.11), residues: 2408 sheet: -0.89 (0.16), residues: 907 loop : -1.16 (0.10), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRPLT 125 HIS 0.008 0.001 HISLE 128 PHE 0.014 0.001 PHELk 34 TYR 0.039 0.002 TYRLT 65 ARG 0.018 0.000 ARGLZ 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1483 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1293 time to evaluate : 6.696 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: LA 208 GLU cc_start: 0.8051 (mp0) cc_final: 0.7737 (pm20) REVERT: LB 70 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8530 (mtpp) REVERT: LB 74 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: LB 167 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: LB 348 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8144 (ptt90) REVERT: LB 351 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7823 (pp) REVERT: LB 360 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7959 (pp) REVERT: LD 86 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.6433 (p90) REVERT: LD 115 MET cc_start: 0.8272 (ptp) cc_final: 0.7956 (ptm) REVERT: LE 245 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7749 (tp-100) REVERT: LG 229 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7603 (ppp80) REVERT: LH 142 ASP cc_start: 0.7371 (p0) cc_final: 0.7054 (p0) REVERT: LJ 12 MET cc_start: 0.7372 (tpp) cc_final: 0.6611 (mpp) REVERT: LN 153 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8631 (mptt) REVERT: LN 204 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6331 (mtt90) REVERT: LO 78 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7937 (mmt180) REVERT: LO 144 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: LP 99 GLU cc_start: 0.7295 (tt0) cc_final: 0.7074 (tt0) REVERT: LR 28 GLU cc_start: 0.7654 (mp0) cc_final: 0.7442 (mm-30) REVERT: LR 31 GLU cc_start: 0.7333 (pm20) cc_final: 0.6762 (pm20) REVERT: LS 80 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8940 (mm) REVERT: LT 104 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.8155 (p) REVERT: LU 44 GLN cc_start: 0.8682 (mp10) cc_final: 0.8457 (pm20) REVERT: LW 1 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6426 (tmm) REVERT: LW 30 GLN cc_start: 0.8102 (mp-120) cc_final: 0.7854 (mm-40) REVERT: LY 65 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: La 106 SER cc_start: 0.8655 (m) cc_final: 0.8329 (m) REVERT: Lb 27 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7575 (mm-40) REVERT: Lb 65 MET cc_start: 0.7319 (mmp) cc_final: 0.7069 (mpp) REVERT: Lc 61 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6661 (tp30) REVERT: Lg 89 ASP cc_start: 0.7398 (m-30) cc_final: 0.7145 (m-30) REVERT: Lh 111 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: Lj 65 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.5983 (mtp180) REVERT: Ln 11 ARG cc_start: 0.7718 (mtt180) cc_final: 0.7248 (tpt-90) REVERT: Ln 17 ARG cc_start: 0.8887 (mtm-85) cc_final: 0.8684 (mtt180) REVERT: Ln 21 ARG cc_start: 0.8892 (mtp180) cc_final: 0.6980 (tpt170) REVERT: Ln 23 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7985 (ptm-80) REVERT: Lp 10 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8831 (tp) REVERT: Lp 33 GLN cc_start: 0.8507 (tt0) cc_final: 0.8175 (tt0) REVERT: Lz 78 LYS cc_start: 0.4192 (mmpt) cc_final: 0.3595 (mmtt) REVERT: Lz 144 MET cc_start: 0.1285 (mtt) cc_final: 0.0117 (mmt) outliers start: 190 outliers final: 125 residues processed: 1399 average time/residue: 2.0927 time to fit residues: 4241.1127 Evaluate side-chains 1407 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1259 time to evaluate : 6.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 4 VAL Chi-restraints excluded: chain LA residue 15 VAL Chi-restraints excluded: chain LA residue 75 LEU Chi-restraints excluded: chain LA residue 102 LEU Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 70 LYS Chi-restraints excluded: chain LB residue 74 GLU Chi-restraints excluded: chain LB residue 135 LYS Chi-restraints excluded: chain LB residue 162 VAL Chi-restraints excluded: chain LB residue 167 GLN Chi-restraints excluded: chain LB residue 194 LEU Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 298 LEU Chi-restraints excluded: chain LB residue 305 THR Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LB residue 348 ARG Chi-restraints excluded: chain LB residue 351 LEU Chi-restraints excluded: chain LB residue 360 LEU Chi-restraints excluded: chain LC residue 138 MET Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 312 ARG Chi-restraints excluded: chain LC residue 319 LEU Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LD residue 86 TYR Chi-restraints excluded: chain LD residue 194 VAL Chi-restraints excluded: chain LD residue 232 THR Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 245 GLN Chi-restraints excluded: chain LE residue 278 THR Chi-restraints excluded: chain LF residue 213 LEU Chi-restraints excluded: chain LG residue 156 VAL Chi-restraints excluded: chain LG residue 192 ARG Chi-restraints excluded: chain LG residue 229 ARG Chi-restraints excluded: chain LG residue 261 LEU Chi-restraints excluded: chain LI residue 71 CYS Chi-restraints excluded: chain LI residue 102 MET Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 133 VAL Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LL residue 59 VAL Chi-restraints excluded: chain LM residue 31 ILE Chi-restraints excluded: chain LM residue 38 VAL Chi-restraints excluded: chain LM residue 70 GLN Chi-restraints excluded: chain LM residue 125 ASN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 149 GLN Chi-restraints excluded: chain LN residue 153 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 164 LEU Chi-restraints excluded: chain LN residue 204 ARG Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 64 THR Chi-restraints excluded: chain LO residue 78 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 141 LEU Chi-restraints excluded: chain LO residue 144 GLU Chi-restraints excluded: chain LP residue 57 CYS Chi-restraints excluded: chain LP residue 76 TRP Chi-restraints excluded: chain LP residue 85 LYS Chi-restraints excluded: chain LP residue 96 LYS Chi-restraints excluded: chain LP residue 110 ASP Chi-restraints excluded: chain LP residue 129 THR Chi-restraints excluded: chain LQ residue 19 LYS Chi-restraints excluded: chain LQ residue 79 THR Chi-restraints excluded: chain LQ residue 114 LEU Chi-restraints excluded: chain LS residue 16 CYS Chi-restraints excluded: chain LS residue 80 ILE Chi-restraints excluded: chain LS residue 85 ASP Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LT residue 29 THR Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 22 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LV residue 20 LEU Chi-restraints excluded: chain LV residue 65 VAL Chi-restraints excluded: chain LV residue 118 THR Chi-restraints excluded: chain LW residue 1 MET Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 54 LEU Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 38 LEU Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 58 VAL Chi-restraints excluded: chain LY residue 65 GLN Chi-restraints excluded: chain LY residue 91 ASN Chi-restraints excluded: chain LZ residue 88 ASP Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain La residue 63 LEU Chi-restraints excluded: chain La residue 132 ARG Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lb residue 27 GLN Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lb residue 51 LYS Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lc residue 61 GLU Chi-restraints excluded: chain Lc residue 65 MET Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 100 ASN Chi-restraints excluded: chain Ld residue 105 LEU Chi-restraints excluded: chain Ld residue 121 ASN Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Le residue 34 ASN Chi-restraints excluded: chain Le residue 45 VAL Chi-restraints excluded: chain Le residue 53 ILE Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Le residue 129 LEU Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 76 ARG Chi-restraints excluded: chain Lg residue 2 VAL Chi-restraints excluded: chain Lg residue 48 VAL Chi-restraints excluded: chain Lg residue 86 CYS Chi-restraints excluded: chain Lh residue 29 SER Chi-restraints excluded: chain Lh residue 110 LYS Chi-restraints excluded: chain Lh residue 111 GLU Chi-restraints excluded: chain Lh residue 116 LEU Chi-restraints excluded: chain Li residue 18 THR Chi-restraints excluded: chain Lj residue 65 ARG Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ln residue 23 ARG Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lp residue 10 ILE Chi-restraints excluded: chain Lr residue 14 SER Chi-restraints excluded: chain Lr residue 21 ASN Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 51 VAL Chi-restraints excluded: chain Lr residue 60 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 101 LYS Chi-restraints excluded: chain Lz residue 148 VAL Chi-restraints excluded: chain Lz residue 172 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 626 optimal weight: 3.9990 chunk 1008 optimal weight: 0.5980 chunk 615 optimal weight: 0.8980 chunk 478 optimal weight: 0.9990 chunk 701 optimal weight: 0.9980 chunk 1058 optimal weight: 10.0000 chunk 973 optimal weight: 4.9990 chunk 842 optimal weight: 0.0980 chunk 87 optimal weight: 10.0000 chunk 650 optimal weight: 0.5980 chunk 516 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 132 ASN LE 250 GLN LE 256 GLN LF 63 GLN LF 163 ASN LG 43 GLN LG 46 GLN LG 64 GLN LG 159 HIS LG 208 ASN ** LH 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 78 GLN LI 133 GLN LI 177 ASN LI 213 HIS ** LJ 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 167 GLN LL 159 ASN LO 180 GLN LS 50 GLN LU 95 ASN LW 48 GLN LX 111 GLN LZ 78 ASN La 85 GLN La 120 GLN Lb 19 ASN Lb 61 ASN Ld 93 ASN Lh 65 GLN Lh 68 ASN Lm 120 ASN Lr 83 ASN Lr 121 GLN Lz 72 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.122 151875 Z= 0.140 Angle : 0.588 26.315 224442 Z= 0.296 Chirality : 0.038 2.512 28025 Planarity : 0.005 0.102 13439 Dihedral : 24.363 179.609 71461 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.59 % Favored : 93.35 % Rotamer: Outliers : 2.45 % Allowed : 27.37 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.17 % Twisted Proline : 1.77 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.10), residues: 6696 helix: 1.38 (0.11), residues: 2411 sheet: -0.81 (0.16), residues: 915 loop : -1.15 (0.10), residues: 3370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRPLT 125 HIS 0.008 0.001 HISLE 128 PHE 0.041 0.001 PHELU 39 TYR 0.037 0.001 TYRLT 65 ARG 0.038 0.000 ARGLE 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1481 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1340 time to evaluate : 6.816 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: LB 167 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: LB 348 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8121 (ptt90) REVERT: LB 351 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7810 (pp) REVERT: LD 115 MET cc_start: 0.8220 (ptp) cc_final: 0.7893 (ptm) REVERT: LE 245 GLN cc_start: 0.8879 (tp40) cc_final: 0.8211 (tp-100) REVERT: LE 249 ASP cc_start: 0.7942 (m-30) cc_final: 0.7627 (m-30) REVERT: LG 229 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7556 (ppp80) REVERT: LH 142 ASP cc_start: 0.7476 (p0) cc_final: 0.7107 (p0) REVERT: LM 50 MET cc_start: 0.7723 (ttm) cc_final: 0.7424 (ttm) REVERT: LN 99 GLN cc_start: 0.8661 (tt0) cc_final: 0.8452 (tt0) REVERT: LN 188 ARG cc_start: 0.8239 (tmm160) cc_final: 0.8022 (ttp80) REVERT: LN 204 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.6337 (mtt90) REVERT: LO 144 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: LR 28 GLU cc_start: 0.7633 (mp0) cc_final: 0.7388 (mm-30) REVERT: LR 31 GLU cc_start: 0.7280 (pm20) cc_final: 0.6720 (pm20) REVERT: LS 80 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8860 (mm) REVERT: LT 104 SER cc_start: 0.8353 (t) cc_final: 0.8148 (p) REVERT: LW 1 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6376 (tmm) REVERT: LW 20 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7848 (ttm-80) REVERT: LW 30 GLN cc_start: 0.8039 (mp-120) cc_final: 0.7637 (mm-40) REVERT: LX 145 ASP cc_start: 0.8034 (t0) cc_final: 0.7830 (t70) REVERT: LX 147 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9095 (tp) REVERT: Lb 65 MET cc_start: 0.7296 (mmp) cc_final: 0.7056 (mpp) REVERT: Lc 61 GLU cc_start: 0.6943 (tp30) cc_final: 0.6665 (tp30) REVERT: Lf 104 MET cc_start: 0.6924 (mmm) cc_final: 0.6644 (mmm) REVERT: Lg 85 LYS cc_start: 0.8044 (ttpp) cc_final: 0.7737 (ttpp) REVERT: Lg 89 ASP cc_start: 0.7378 (m-30) cc_final: 0.7172 (m-30) REVERT: Lj 65 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.5724 (mtp180) REVERT: Ln 10 MET cc_start: 0.7594 (tpt) cc_final: 0.7206 (tpt) REVERT: Ln 11 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7206 (tpt-90) REVERT: Ln 21 ARG cc_start: 0.8844 (mtp180) cc_final: 0.7154 (tpt170) REVERT: Ln 23 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8072 (ptm-80) REVERT: Lp 10 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8752 (tp) REVERT: Lp 33 GLN cc_start: 0.8382 (tt0) cc_final: 0.8060 (tt0) REVERT: Lz 78 LYS cc_start: 0.4127 (mmpt) cc_final: 0.3578 (mmtt) REVERT: Lz 144 MET cc_start: 0.1459 (mtt) cc_final: 0.0232 (mmt) outliers start: 141 outliers final: 87 residues processed: 1421 average time/residue: 2.0890 time to fit residues: 4277.8616 Evaluate side-chains 1369 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1270 time to evaluate : 6.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 4 VAL Chi-restraints excluded: chain LA residue 15 VAL Chi-restraints excluded: chain LA residue 102 LEU Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 135 LYS Chi-restraints excluded: chain LB residue 167 GLN Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LB residue 348 ARG Chi-restraints excluded: chain LB residue 351 LEU Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LD residue 194 VAL Chi-restraints excluded: chain LD residue 232 THR Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LD residue 293 ARG Chi-restraints excluded: chain LE residue 258 LEU Chi-restraints excluded: chain LE residue 278 THR Chi-restraints excluded: chain LF residue 213 LEU Chi-restraints excluded: chain LG residue 156 VAL Chi-restraints excluded: chain LG residue 229 ARG Chi-restraints excluded: chain LG residue 261 LEU Chi-restraints excluded: chain LI residue 71 CYS Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 133 VAL Chi-restraints excluded: chain LL residue 59 VAL Chi-restraints excluded: chain LM residue 38 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 164 LEU Chi-restraints excluded: chain LN residue 204 ARG Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 141 LEU Chi-restraints excluded: chain LO residue 144 GLU Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 57 CYS Chi-restraints excluded: chain LP residue 129 THR Chi-restraints excluded: chain LQ residue 19 LYS Chi-restraints excluded: chain LQ residue 79 THR Chi-restraints excluded: chain LQ residue 114 LEU Chi-restraints excluded: chain LS residue 16 CYS Chi-restraints excluded: chain LS residue 50 GLN Chi-restraints excluded: chain LS residue 80 ILE Chi-restraints excluded: chain LS residue 85 ASP Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LU residue 22 THR Chi-restraints excluded: chain LV residue 20 LEU Chi-restraints excluded: chain LV residue 65 VAL Chi-restraints excluded: chain LV residue 118 THR Chi-restraints excluded: chain LW residue 1 MET Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 54 LEU Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LX residue 147 LEU Chi-restraints excluded: chain LY residue 38 LEU Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 58 VAL Chi-restraints excluded: chain LY residue 91 ASN Chi-restraints excluded: chain LZ residue 92 ASP Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lc residue 26 LYS Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 100 ASN Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Le residue 34 ASN Chi-restraints excluded: chain Le residue 53 ILE Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Le residue 129 LEU Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lg residue 2 VAL Chi-restraints excluded: chain Lg residue 86 CYS Chi-restraints excluded: chain Lh residue 29 SER Chi-restraints excluded: chain Lh residue 110 LYS Chi-restraints excluded: chain Lh residue 111 GLU Chi-restraints excluded: chain Lj residue 65 ARG Chi-restraints excluded: chain Ln residue 23 ARG Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lp residue 10 ILE Chi-restraints excluded: chain Lr residue 43 LEU Chi-restraints excluded: chain Lr residue 49 VAL Chi-restraints excluded: chain Lr residue 51 VAL Chi-restraints excluded: chain Lr residue 60 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lz residue 148 VAL Chi-restraints excluded: chain Lz residue 172 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 669 optimal weight: 3.9990 chunk 897 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 776 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 843 optimal weight: 50.0000 chunk 353 optimal weight: 10.0000 chunk 866 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 132 ASN LB 289 GLN LB 302 ASN LB 328 ASN LC 276 ASN LD 225 GLN LD 282 GLN LE 167 GLN ** LE 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 250 GLN LE 256 GLN LF 63 GLN LF 163 ASN LG 43 GLN LG 46 GLN LG 64 GLN LG 159 HIS LG 208 ASN LG 227 ASN ** LH 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 163 GLN LI 177 ASN LI 213 HIS ** LJ 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 167 GLN LL 159 ASN ** LM 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 180 GLN LO 184 ASN ** LS 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 125 GLN LU 27 HIS LW 48 GLN LX 94 ASN LX 111 GLN LX 125 ASN LY 14 ASN LZ 78 ASN La 67 GLN Lb 19 ASN Lb 61 ASN Ld 93 ASN Lh 65 GLN Lh 68 ASN Lh 108 GLN Lm 120 ASN Lz 72 GLN Lz 119 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.072761 restraints weight = 204383.129| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 0.98 r_work: 0.2523 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 151875 Z= 0.442 Angle : 0.721 24.249 224442 Z= 0.363 Chirality : 0.047 2.598 28025 Planarity : 0.006 0.109 13439 Dihedral : 24.400 179.540 71461 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.90 % Favored : 93.01 % Rotamer: Outliers : 2.78 % Allowed : 27.63 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.17 % Twisted Proline : 1.77 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 6696 helix: 1.17 (0.11), residues: 2420 sheet: -0.86 (0.16), residues: 907 loop : -1.16 (0.10), residues: 3369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRPLT 125 HIS 0.020 0.002 HISLE 128 PHE 0.023 0.002 PHELD 3 TYR 0.043 0.003 TYRLT 65 ARG 0.021 0.001 ARGLZ 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 59010.28 seconds wall clock time: 1018 minutes 44.50 seconds (61124.50 seconds total)