Starting phenix.real_space_refine on Thu Jun 27 05:52:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bru_44844/06_2024/9bru_44844.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bru_44844/06_2024/9bru_44844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bru_44844/06_2024/9bru_44844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bru_44844/06_2024/9bru_44844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bru_44844/06_2024/9bru_44844.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bru_44844/06_2024/9bru_44844.pdb" } resolution = 4.4 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 387 5.16 5 C 41941 2.51 5 N 11101 2.21 5 O 12119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "7 GLU 8": "OE1" <-> "OE2" Residue "7 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 129": "OE1" <-> "OE2" Residue "7 GLU 143": "OE1" <-> "OE2" Residue "7 GLU 173": "OE1" <-> "OE2" Residue "8 GLU 28": "OE1" <-> "OE2" Residue "8 GLU 58": "OE1" <-> "OE2" Residue "8 GLU 65": "OE1" <-> "OE2" Residue "8 ASP 88": "OD1" <-> "OD2" Residue "8 ASP 164": "OD1" <-> "OD2" Residue "8 GLU 175": "OE1" <-> "OE2" Residue "8 GLU 176": "OE1" <-> "OE2" Residue "9 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 55": "OE1" <-> "OE2" Residue "9 GLU 61": "OE1" <-> "OE2" Residue "9 TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 162": "OD1" <-> "OD2" Residue "9 GLU 170": "OE1" <-> "OE2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 97": "OE1" <-> "OE2" Residue "Q PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 176": "OE1" <-> "OE2" Residue "Q GLU 197": "OE1" <-> "OE2" Residue "Q ASP 226": "OD1" <-> "OD2" Residue "R ASP 24": "OD1" <-> "OD2" Residue "R GLU 38": "OE1" <-> "OE2" Residue "R GLU 105": "OE1" <-> "OE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T GLU 72": "OE1" <-> "OE2" Residue "V PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 72": "OE1" <-> "OE2" Residue "6 GLU 12": "OE1" <-> "OE2" Residue "6 ASP 82": "OD1" <-> "OD2" Residue "6 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 257": "OE1" <-> "OE2" Residue "6 GLU 264": "OE1" <-> "OE2" Residue "U GLU 298": "OE1" <-> "OE2" Residue "U GLU 340": "OE1" <-> "OE2" Residue "U PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 429": "OE1" <-> "OE2" Residue "U ASP 445": "OD1" <-> "OD2" Residue "a GLU 28": "OE1" <-> "OE2" Residue "a PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 60": "OE1" <-> "OE2" Residue "a GLU 69": "OE1" <-> "OE2" Residue "a PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 102": "OE1" <-> "OE2" Residue "a GLU 110": "OE1" <-> "OE2" Residue "a PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 214": "OE1" <-> "OE2" Residue "a ASP 215": "OD1" <-> "OD2" Residue "a PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 263": "OE1" <-> "OE2" Residue "a TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 329": "OE1" <-> "OE2" Residue "a PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 499": "OE1" <-> "OE2" Residue "a PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 728": "OE1" <-> "OE2" Residue "e PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 116": "OE1" <-> "OE2" Residue "g TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 9": "OE1" <-> "OE2" Residue "i PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 139": "OE1" <-> "OE2" Residue "k GLU 50": "OE1" <-> "OE2" Residue "k ASP 115": "OD1" <-> "OD2" Residue "k PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 9": "OE1" <-> "OE2" Residue "n TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 107": "OD1" <-> "OD2" Residue "d GLU 149": "OE1" <-> "OE2" Residue "d PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 217": "OD1" <-> "OD2" Residue "d TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 302": "OE1" <-> "OE2" Residue "p TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 49": "OE1" <-> "OE2" Residue "1 ASP 108": "OD1" <-> "OD2" Residue "1 TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 193": "OE1" <-> "OE2" Residue "1 TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 293": "OE1" <-> "OE2" Residue "1 PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 356": "OE1" <-> "OE2" Residue "1 GLU 360": "OE1" <-> "OE2" Residue "1 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 401": "OE1" <-> "OE2" Residue "1 PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 49": "OE1" <-> "OE2" Residue "0 GLU 58": "OE1" <-> "OE2" Residue "0 ASP 108": "OD1" <-> "OD2" Residue "0 ASP 130": "OD1" <-> "OD2" Residue "0 GLU 134": "OE1" <-> "OE2" Residue "0 GLU 195": "OE1" <-> "OE2" Residue "0 GLU 197": "OE1" <-> "OE2" Residue "0 GLU 201": "OE1" <-> "OE2" Residue "0 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 219": "OE1" <-> "OE2" Residue "0 GLU 360": "OE1" <-> "OE2" Residue "0 GLU 367": "OE1" <-> "OE2" Residue "0 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 401": "OE1" <-> "OE2" Residue "0 TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 471": "OE1" <-> "OE2" Residue "0 PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 594": "OE1" <-> "OE2" Residue "2 GLU 41": "OE1" <-> "OE2" Residue "2 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 195": "OE1" <-> "OE2" Residue "2 GLU 297": "OE1" <-> "OE2" Residue "2 GLU 387": "OE1" <-> "OE2" Residue "2 GLU 401": "OE1" <-> "OE2" Residue "2 TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 471": "OE1" <-> "OE2" Residue "2 ASP 505": "OD1" <-> "OD2" Residue "2 PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 100": "OE1" <-> "OE2" Residue "3 GLU 113": "OE1" <-> "OE2" Residue "3 GLU 125": "OE1" <-> "OE2" Residue "3 GLU 167": "OE1" <-> "OE2" Residue "3 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 247": "OD1" <-> "OD2" Residue "3 ASP 255": "OD1" <-> "OD2" Residue "3 GLU 270": "OE1" <-> "OE2" Residue "3 TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 316": "OE1" <-> "OE2" Residue "3 TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 61": "OD1" <-> "OD2" Residue "4 ASP 117": "OD1" <-> "OD2" Residue "4 GLU 125": "OE1" <-> "OE2" Residue "4 PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 168": "OE1" <-> "OE2" Residue "4 ASP 221": "OD1" <-> "OD2" Residue "4 PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 239": "OE1" <-> "OE2" Residue "4 ASP 247": "OD1" <-> "OD2" Residue "4 GLU 249": "OE1" <-> "OE2" Residue "4 GLU 336": "OE1" <-> "OE2" Residue "4 GLU 374": "OE1" <-> "OE2" Residue "4 GLU 459": "OE1" <-> "OE2" Residue "4 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 469": "OE1" <-> "OE2" Residue "4 PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 61": "OD1" <-> "OD2" Residue "5 GLU 70": "OE1" <-> "OE2" Residue "5 ASP 78": "OD1" <-> "OD2" Residue "5 ASP 106": "OD1" <-> "OD2" Residue "5 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 225": "OE1" <-> "OE2" Residue "5 TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 336": "OE1" <-> "OE2" Residue "5 ASP 367": "OD1" <-> "OD2" Residue "5 TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 65548 Number of models: 1 Model: "" Number of chains: 32 Chain: "7" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1676 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain: "8" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "9" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "Q" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "R" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "T" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "V" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "6" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2931 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 9, 'TRANS': 351} Chain breaks: 1 Chain: "U" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3501 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 8, 'TRANS': 417} Chain breaks: 1 Chain: "a" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6117 Classifications: {'peptide': 752} Link IDs: {'PTRANS': 31, 'TRANS': 720} Chain breaks: 2 Chain: "e" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 623 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "f" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "b" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1484 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain: "g" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "X" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "d" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2842 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain: "c" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1642 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "p" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "1" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "0" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4671 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain: "2" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "3" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3610 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 433} Chain breaks: 1 Chain: "4" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3667 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "5" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3667 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Time building chain proxies: 26.44, per 1000 atoms: 0.40 Number of scatterers: 65548 At special positions: 0 Unit cell: (161.534, 182.556, 300.941, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 387 16.00 O 12119 8.00 N 11101 7.00 C 41941 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: 21.55 Conformation dependent library (CDL) restraints added in 8.6 seconds 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15510 Finding SS restraints... Secondary structure from input PDB file: 312 helices and 42 sheets defined 61.2% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain '7' and resid 12 through 48 Processing helix chain '7' and resid 50 through 77 Processing helix chain '7' and resid 79 through 86 Processing helix chain '7' and resid 128 through 175 removed outlier: 3.518A pdb=" N GLU 7 143 " --> pdb=" O ALA 7 139 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP 7 159 " --> pdb=" O PHE 7 155 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLU 7 160 " --> pdb=" O VAL 7 156 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA 7 161 " --> pdb=" O THR 7 157 " (cutoff:3.500A) Processing helix chain '7' and resid 175 through 210 removed outlier: 3.578A pdb=" N ARG 7 179 " --> pdb=" O VAL 7 175 " (cutoff:3.500A) Processing helix chain '8' and resid 3 through 106 removed outlier: 4.104A pdb=" N LYS 8 52 " --> pdb=" O THR 8 48 " (cutoff:3.500A) Processing helix chain '8' and resid 108 through 128 removed outlier: 3.657A pdb=" N VAL 8 114 " --> pdb=" O THR 8 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU 8 128 " --> pdb=" O LEU 8 124 " (cutoff:3.500A) Processing helix chain '8' and resid 140 through 160 removed outlier: 3.571A pdb=" N ALA 8 146 " --> pdb=" O PRO 8 142 " (cutoff:3.500A) Proline residue: 8 153 - end of helix Processing helix chain '8' and resid 196 through 207 Processing helix chain '8' and resid 207 through 217 Processing helix chain '9' and resid 6 through 107 removed outlier: 4.142A pdb=" N LYS 9 107 " --> pdb=" O SER 9 103 " (cutoff:3.500A) Processing helix chain '9' and resid 108 through 128 removed outlier: 3.988A pdb=" N VAL 9 114 " --> pdb=" O THR 9 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 9 128 " --> pdb=" O LEU 9 124 " (cutoff:3.500A) Processing helix chain '9' and resid 137 through 139 No H-bonds generated for 'chain '9' and resid 137 through 139' Processing helix chain '9' and resid 140 through 160 Proline residue: 9 153 - end of helix Processing helix chain '9' and resid 196 through 207 Processing helix chain '9' and resid 207 through 217 Processing helix chain 'Q' and resid 4 through 44 removed outlier: 4.450A pdb=" N VAL Q 8 " --> pdb=" O SER Q 4 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE Q 18 " --> pdb=" O HIS Q 14 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN Q 21 " --> pdb=" O ALA Q 17 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA Q 23 " --> pdb=" O ILE Q 19 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 107 removed outlier: 4.151A pdb=" N LYS Q 107 " --> pdb=" O SER Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 128 removed outlier: 4.209A pdb=" N GLN Q 113 " --> pdb=" O THR Q 109 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL Q 114 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU Q 128 " --> pdb=" O LEU Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 139 No H-bonds generated for 'chain 'Q' and resid 137 through 139' Processing helix chain 'Q' and resid 140 through 160 Proline residue: Q 153 - end of helix Processing helix chain 'Q' and resid 195 through 207 Processing helix chain 'Q' and resid 207 through 217 Processing helix chain 'R' and resid 5 through 103 removed outlier: 3.661A pdb=" N LEU R 11 " --> pdb=" O GLY R 7 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY R 64 " --> pdb=" O GLN R 60 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN R 91 " --> pdb=" O SER R 87 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLU R 93 " --> pdb=" O GLN R 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG R 94 " --> pdb=" O ARG R 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 91 removed outlier: 3.719A pdb=" N ASN T 91 " --> pdb=" O SER T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 105 removed outlier: 3.536A pdb=" N LEU T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 91 removed outlier: 3.874A pdb=" N ARG V 90 " --> pdb=" O SER V 86 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASN V 91 " --> pdb=" O SER V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 91 through 105 removed outlier: 3.927A pdb=" N VAL V 95 " --> pdb=" O ASN V 91 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 23 removed outlier: 4.336A pdb=" N LYS 6 21 " --> pdb=" O GLN 6 17 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS 6 23 " --> pdb=" O TRP 6 19 " (cutoff:3.500A) Processing helix chain '6' and resid 50 through 79 Processing helix chain '6' and resid 92 through 96 removed outlier: 3.876A pdb=" N GLY 6 95 " --> pdb=" O LEU 6 92 " (cutoff:3.500A) Processing helix chain '6' and resid 97 through 103 Processing helix chain '6' and resid 117 through 157 Processing helix chain '6' and resid 171 through 175 removed outlier: 3.980A pdb=" N PHE 6 175 " --> pdb=" O LYS 6 172 " (cutoff:3.500A) Processing helix chain '6' and resid 193 through 205 removed outlier: 3.724A pdb=" N TRP 6 197 " --> pdb=" O ASN 6 193 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE 6 198 " --> pdb=" O HIS 6 194 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS 6 199 " --> pdb=" O ASN 6 195 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU 6 202 " --> pdb=" O ILE 6 198 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N THR 6 203 " --> pdb=" O LYS 6 199 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA 6 205 " --> pdb=" O TYR 6 201 " (cutoff:3.500A) Processing helix chain '6' and resid 232 through 242 removed outlier: 4.067A pdb=" N ASP 6 236 " --> pdb=" O LYS 6 232 " (cutoff:3.500A) Processing helix chain '6' and resid 243 through 245 No H-bonds generated for 'chain '6' and resid 243 through 245' Processing helix chain '6' and resid 254 through 310 Proline residue: 6 278 - end of helix Processing helix chain '6' and resid 327 through 344 removed outlier: 4.261A pdb=" N HIS 6 341 " --> pdb=" O GLU 6 337 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU 6 342 " --> pdb=" O LEU 6 338 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP 6 343 " --> pdb=" O TYR 6 339 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 27 Processing helix chain 'U' and resid 33 through 37 Processing helix chain 'U' and resid 45 through 52 removed outlier: 3.674A pdb=" N PHE U 49 " --> pdb=" O GLU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 65 Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'U' and resid 79 through 84 removed outlier: 3.591A pdb=" N ILE U 84 " --> pdb=" O LEU U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 103 removed outlier: 3.793A pdb=" N GLN U 91 " --> pdb=" O GLU U 87 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR U 92 " --> pdb=" O GLN U 88 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU U 103 " --> pdb=" O ASP U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 118 through 122 removed outlier: 3.822A pdb=" N THR U 121 " --> pdb=" O SER U 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 146 Processing helix chain 'U' and resid 158 through 163 Processing helix chain 'U' and resid 164 through 169 removed outlier: 4.051A pdb=" N ILE U 168 " --> pdb=" O TYR U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 170 through 172 No H-bonds generated for 'chain 'U' and resid 170 through 172' Processing helix chain 'U' and resid 196 through 209 Processing helix chain 'U' and resid 211 through 221 removed outlier: 3.993A pdb=" N ALA U 217 " --> pdb=" O GLU U 213 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA U 221 " --> pdb=" O ALA U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 222 through 233 Processing helix chain 'U' and resid 236 through 251 removed outlier: 3.704A pdb=" N GLN U 240 " --> pdb=" O GLY U 236 " (cutoff:3.500A) Processing helix chain 'U' and resid 253 through 261 Processing helix chain 'U' and resid 264 through 276 Processing helix chain 'U' and resid 279 through 296 Processing helix chain 'U' and resid 298 through 302 Processing helix chain 'U' and resid 303 through 311 removed outlier: 4.033A pdb=" N MET U 309 " --> pdb=" O TYR U 305 " (cutoff:3.500A) Processing helix chain 'U' and resid 313 through 322 removed outlier: 3.670A pdb=" N GLN U 317 " --> pdb=" O LYS U 313 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN U 320 " --> pdb=" O LYS U 316 " (cutoff:3.500A) Processing helix chain 'U' and resid 328 through 350 removed outlier: 3.838A pdb=" N SER U 332 " --> pdb=" O ASP U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 351 through 362 removed outlier: 3.687A pdb=" N GLY U 362 " --> pdb=" O GLU U 358 " (cutoff:3.500A) Processing helix chain 'U' and resid 367 through 371 Processing helix chain 'U' and resid 372 through 379 Processing helix chain 'U' and resid 380 through 384 Processing helix chain 'U' and resid 388 through 401 Processing helix chain 'U' and resid 403 through 419 Processing helix chain 'U' and resid 421 through 432 Processing helix chain 'U' and resid 432 through 441 removed outlier: 3.569A pdb=" N LEU U 436 " --> pdb=" O GLY U 432 " (cutoff:3.500A) Processing helix chain 'U' and resid 445 through 459 Processing helix chain 'a' and resid 19 through 33 removed outlier: 3.915A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER a 27 " --> pdb=" O TYR a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 76 Processing helix chain 'a' and resid 92 through 132 removed outlier: 4.186A pdb=" N ASP a 96 " --> pdb=" O ARG a 92 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA a 117 " --> pdb=" O THR a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 199 removed outlier: 3.774A pdb=" N ARG a 192 " --> pdb=" O PRO a 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 248 removed outlier: 4.239A pdb=" N LYS a 241 " --> pdb=" O LYS a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 258 through 316 removed outlier: 4.043A pdb=" N LYS a 262 " --> pdb=" O PRO a 258 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP a 273 " --> pdb=" O ASN a 269 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP a 274 " --> pdb=" O THR a 270 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU a 290 " --> pdb=" O ARG a 286 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN a 291 " --> pdb=" O GLN a 287 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA a 292 " --> pdb=" O ARG a 288 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA a 293 " --> pdb=" O VAL a 289 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN a 296 " --> pdb=" O ALA a 292 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG a 298 " --> pdb=" O ALA a 294 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL a 299 " --> pdb=" O LYS a 295 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU a 316 " --> pdb=" O HIS a 312 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 351 Processing helix chain 'a' and resid 378 through 389 removed outlier: 3.646A pdb=" N TYR a 388 " --> pdb=" O ILE a 384 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 414 Proline residue: a 407 - end of helix Processing helix chain 'a' and resid 417 through 433 Processing helix chain 'a' and resid 433 through 440 removed outlier: 3.574A pdb=" N GLN a 440 " --> pdb=" O ARG a 436 " (cutoff:3.500A) Processing helix chain 'a' and resid 444 through 453 Processing helix chain 'a' and resid 453 through 472 removed outlier: 3.905A pdb=" N ASN a 472 " --> pdb=" O GLY a 468 " (cutoff:3.500A) Processing helix chain 'a' and resid 527 through 532 removed outlier: 3.546A pdb=" N ILE a 532 " --> pdb=" O ILE a 529 " (cutoff:3.500A) Processing helix chain 'a' and resid 533 through 534 No H-bonds generated for 'chain 'a' and resid 533 through 534' Processing helix chain 'a' and resid 535 through 562 Processing helix chain 'a' and resid 562 through 570 removed outlier: 4.439A pdb=" N ASN a 566 " --> pdb=" O LEU a 562 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE a 570 " --> pdb=" O ASN a 566 " (cutoff:3.500A) Processing helix chain 'a' and resid 573 through 578 removed outlier: 4.181A pdb=" N PHE a 578 " --> pdb=" O LEU a 574 " (cutoff:3.500A) Processing helix chain 'a' and resid 579 through 605 removed outlier: 4.962A pdb=" N TYR a 593 " --> pdb=" O SER a 589 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU a 594 " --> pdb=" O LEU a 590 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR a 603 " --> pdb=" O PHE a 599 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR a 605 " --> pdb=" O LYS a 601 " (cutoff:3.500A) Processing helix chain 'a' and resid 606 through 613 removed outlier: 5.682A pdb=" N ARG a 611 " --> pdb=" O HIS a 608 " (cutoff:3.500A) Processing helix chain 'a' and resid 617 through 625 Processing helix chain 'a' and resid 639 through 653 removed outlier: 3.512A pdb=" N PHE a 646 " --> pdb=" O GLY a 642 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL a 649 " --> pdb=" O CYS a 645 " (cutoff:3.500A) Processing helix chain 'a' and resid 661 through 674 Processing helix chain 'a' and resid 716 through 739 removed outlier: 4.400A pdb=" N ILE a 734 " --> pdb=" O CYS a 730 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER a 735 " --> pdb=" O LEU a 731 " (cutoff:3.500A) Processing helix chain 'a' and resid 740 through 762 removed outlier: 4.211A pdb=" N TRP a 744 " --> pdb=" O TYR a 740 " (cutoff:3.500A) Processing helix chain 'a' and resid 769 through 791 removed outlier: 4.165A pdb=" N LEU a 775 " --> pdb=" O LEU a 771 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY a 776 " --> pdb=" O ALA a 772 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE a 779 " --> pdb=" O LEU a 775 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA a 782 " --> pdb=" O PHE a 778 " (cutoff:3.500A) Processing helix chain 'a' and resid 793 through 817 removed outlier: 3.744A pdb=" N GLN a 813 " --> pdb=" O TRP a 809 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN a 814 " --> pdb=" O VAL a 810 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE a 816 " --> pdb=" O PHE a 812 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 23 Processing helix chain 'e' and resid 23 through 28 Processing helix chain 'e' and resid 33 through 59 removed outlier: 4.106A pdb=" N GLN e 59 " --> pdb=" O ALA e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 78 Processing helix chain 'f' and resid 8 through 36 removed outlier: 4.255A pdb=" N ILE f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 44 Processing helix chain 'f' and resid 59 through 90 removed outlier: 3.725A pdb=" N ASN f 90 " --> pdb=" O GLN f 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 29 removed outlier: 4.005A pdb=" N PHE b 29 " --> pdb=" O CYS b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 35 Processing helix chain 'b' and resid 36 through 44 removed outlier: 4.141A pdb=" N THR b 44 " --> pdb=" O PHE b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 81 removed outlier: 3.676A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL b 81 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 91 Processing helix chain 'b' and resid 91 through 114 removed outlier: 3.898A pdb=" N MET b 107 " --> pdb=" O TYR b 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 169 removed outlier: 3.690A pdb=" N GLY b 161 " --> pdb=" O ILE b 157 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU b 164 " --> pdb=" O SER b 160 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA b 167 " --> pdb=" O ALA b 163 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN b 169 " --> pdb=" O ALA b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 176 removed outlier: 4.437A pdb=" N VAL b 174 " --> pdb=" O SER b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 177 through 200 removed outlier: 3.726A pdb=" N ARG b 200 " --> pdb=" O LEU b 196 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 48 removed outlier: 4.227A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA g 43 " --> pdb=" O THR g 39 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET g 47 " --> pdb=" O ALA g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 56 through 62 Processing helix chain 'g' and resid 63 through 79 Processing helix chain 'g' and resid 88 through 121 Processing helix chain 'g' and resid 124 through 126 No H-bonds generated for 'chain 'g' and resid 124 through 126' Processing helix chain 'g' and resid 127 through 155 removed outlier: 3.579A pdb=" N ALA g 138 " --> pdb=" O ILE g 134 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL g 148 " --> pdb=" O TYR g 144 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS g 155 " --> pdb=" O ILE g 151 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 46 removed outlier: 4.444A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL h 16 " --> pdb=" O SER h 12 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL h 46 " --> pdb=" O ALA h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 63 Proline residue: h 58 - end of helix removed outlier: 3.893A pdb=" N GLY h 63 " --> pdb=" O VAL h 59 " (cutoff:3.500A) Processing helix chain 'h' and resid 63 through 80 Processing helix chain 'h' and resid 88 through 122 removed outlier: 3.689A pdb=" N PHE h 108 " --> pdb=" O LEU h 104 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA h 109 " --> pdb=" O ALA h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 126 through 139 removed outlier: 4.632A pdb=" N GLY h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) Processing helix chain 'h' and resid 139 through 154 Processing helix chain 'i' and resid 13 through 45 Processing helix chain 'i' and resid 46 through 47 No H-bonds generated for 'chain 'i' and resid 46 through 47' Processing helix chain 'i' and resid 48 through 50 No H-bonds generated for 'chain 'i' and resid 48 through 50' Processing helix chain 'i' and resid 51 through 62 removed outlier: 4.535A pdb=" N ILE i 57 " --> pdb=" O MET i 53 " (cutoff:3.500A) Proline residue: i 58 - end of helix Processing helix chain 'i' and resid 63 through 80 Processing helix chain 'i' and resid 87 through 121 removed outlier: 4.120A pdb=" N LEU i 91 " --> pdb=" O TYR i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 122 through 123 No H-bonds generated for 'chain 'i' and resid 122 through 123' Processing helix chain 'i' and resid 124 through 125 No H-bonds generated for 'chain 'i' and resid 124 through 125' Processing helix chain 'i' and resid 126 through 155 removed outlier: 4.416A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 48 removed outlier: 3.743A pdb=" N MET j 23 " --> pdb=" O ALA j 19 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 62 Processing helix chain 'j' and resid 63 through 80 Processing helix chain 'j' and resid 88 through 122 Processing helix chain 'j' and resid 124 through 126 No H-bonds generated for 'chain 'j' and resid 124 through 126' Processing helix chain 'j' and resid 127 through 139 Processing helix chain 'j' and resid 139 through 155 removed outlier: 4.064A pdb=" N LEU j 143 " --> pdb=" O GLU j 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 43 removed outlier: 3.787A pdb=" N THR k 39 " --> pdb=" O ALA k 35 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE k 41 " --> pdb=" O SER k 37 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA k 42 " --> pdb=" O GLY k 38 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA k 43 " --> pdb=" O THR k 39 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 55 removed outlier: 3.935A pdb=" N LEU k 51 " --> pdb=" O ARG k 48 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE k 52 " --> pdb=" O PRO k 49 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N MET k 53 " --> pdb=" O GLU k 50 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER k 55 " --> pdb=" O ILE k 52 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 80 Processing helix chain 'k' and resid 88 through 121 removed outlier: 3.695A pdb=" N ALA k 116 " --> pdb=" O ILE k 112 " (cutoff:3.500A) Processing helix chain 'k' and resid 124 through 126 No H-bonds generated for 'chain 'k' and resid 124 through 126' Processing helix chain 'k' and resid 127 through 155 removed outlier: 3.636A pdb=" N VAL k 140 " --> pdb=" O ILE k 136 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU k 141 " --> pdb=" O PHE k 137 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY k 142 " --> pdb=" O ALA k 138 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 43 removed outlier: 4.080A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 79 removed outlier: 4.885A pdb=" N GLY l 63 " --> pdb=" O VAL l 59 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE l 64 " --> pdb=" O VAL l 60 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE l 65 " --> pdb=" O MET l 61 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA l 66 " --> pdb=" O ALA l 62 " (cutoff:3.500A) Processing helix chain 'l' and resid 88 through 120 removed outlier: 4.232A pdb=" N VAL l 118 " --> pdb=" O GLY l 114 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 126 No H-bonds generated for 'chain 'l' and resid 124 through 126' Processing helix chain 'l' and resid 127 through 152 removed outlier: 3.672A pdb=" N GLY l 145 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU l 146 " --> pdb=" O GLY l 142 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU l 152 " --> pdb=" O VAL l 148 " (cutoff:3.500A) Processing helix chain 'm' and resid 11 through 45 Processing helix chain 'm' and resid 46 through 47 No H-bonds generated for 'chain 'm' and resid 46 through 47' Processing helix chain 'm' and resid 48 through 50 No H-bonds generated for 'chain 'm' and resid 48 through 50' Processing helix chain 'm' and resid 51 through 56 Processing helix chain 'm' and resid 58 through 80 removed outlier: 4.465A pdb=" N ILE m 65 " --> pdb=" O MET m 61 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA m 66 " --> pdb=" O ALA m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 120 removed outlier: 4.328A pdb=" N PHE m 90 " --> pdb=" O LEU m 86 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY m 120 " --> pdb=" O ALA m 116 " (cutoff:3.500A) Processing helix chain 'm' and resid 127 through 154 removed outlier: 4.428A pdb=" N MET m 131 " --> pdb=" O LEU m 127 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 45 Processing helix chain 'n' and resid 53 through 55 No H-bonds generated for 'chain 'n' and resid 53 through 55' Processing helix chain 'n' and resid 56 through 80 removed outlier: 4.075A pdb=" N ALA n 62 " --> pdb=" O PRO n 58 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY n 63 " --> pdb=" O VAL n 59 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE n 65 " --> pdb=" O MET n 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 88 through 122 Processing helix chain 'n' and resid 123 through 126 removed outlier: 6.915A pdb=" N ARG n 126 " --> pdb=" O GLN n 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 123 through 126' Processing helix chain 'n' and resid 127 through 154 removed outlier: 3.607A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 46 removed outlier: 4.630A pdb=" N VAL o 46 " --> pdb=" O ALA o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.705A pdb=" N ILE o 65 " --> pdb=" O MET o 61 " (cutoff:3.500A) Processing helix chain 'o' and resid 88 through 122 removed outlier: 3.804A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA o 122 " --> pdb=" O VAL o 118 " (cutoff:3.500A) Processing helix chain 'o' and resid 123 through 126 removed outlier: 6.543A pdb=" N ARG o 126 " --> pdb=" O GLN o 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 123 through 126' Processing helix chain 'o' and resid 127 through 155 removed outlier: 4.096A pdb=" N ILE o 132 " --> pdb=" O PHE o 128 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU o 133 " --> pdb=" O VAL o 129 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU o 135 " --> pdb=" O MET o 131 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY o 145 " --> pdb=" O LEU o 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 23 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 68 through 74 removed outlier: 3.550A pdb=" N VAL X 74 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 74 through 80 Processing helix chain 'X' and resid 103 through 109 Processing helix chain 'd' and resid 8 through 24 removed outlier: 5.474A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU d 19 " --> pdb=" O TYR d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 27 No H-bonds generated for 'chain 'd' and resid 25 through 27' Processing helix chain 'd' and resid 29 through 37 removed outlier: 3.867A pdb=" N ASN d 35 " --> pdb=" O ALA d 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 51 Processing helix chain 'd' and resid 67 through 87 Processing helix chain 'd' and resid 90 through 113 removed outlier: 4.155A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 119 Processing helix chain 'd' and resid 121 through 126 removed outlier: 3.802A pdb=" N LEU d 125 " --> pdb=" O SER d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 134 Processing helix chain 'd' and resid 146 through 158 removed outlier: 4.256A pdb=" N ASP d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 165 Processing helix chain 'd' and resid 169 through 174 removed outlier: 3.660A pdb=" N ASP d 174 " --> pdb=" O GLU d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 177 through 200 Processing helix chain 'd' and resid 202 through 228 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 233 through 241 Processing helix chain 'd' and resid 251 through 258 removed outlier: 3.658A pdb=" N ARG d 257 " --> pdb=" O ALA d 253 " (cutoff:3.500A) Processing helix chain 'd' and resid 260 through 269 Processing helix chain 'd' and resid 271 through 281 removed outlier: 4.171A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 308 removed outlier: 4.094A pdb=" N ASN d 308 " --> pdb=" O LEU d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 315 removed outlier: 3.769A pdb=" N VAL d 314 " --> pdb=" O HIS d 311 " (cutoff:3.500A) Processing helix chain 'd' and resid 316 through 339 Processing helix chain 'c' and resid 278 through 283 removed outlier: 3.673A pdb=" N THR c 283 " --> pdb=" O THR c 280 " (cutoff:3.500A) Processing helix chain 'c' and resid 419 through 441 removed outlier: 3.882A pdb=" N PHE c 428 " --> pdb=" O LEU c 424 " (cutoff:3.500A) Processing helix chain 'p' and resid 300 through 330 removed outlier: 4.119A pdb=" N SER p 304 " --> pdb=" O ASN p 300 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL p 305 " --> pdb=" O LEU p 301 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 114 Processing helix chain '1' and resid 255 through 266 removed outlier: 4.000A pdb=" N ILE 1 259 " --> pdb=" O GLY 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 291 removed outlier: 3.856A pdb=" N MET 1 284 " --> pdb=" O ARG 1 280 " (cutoff:3.500A) Processing helix chain '1' and resid 321 through 339 removed outlier: 3.523A pdb=" N ILE 1 327 " --> pdb=" O ARG 1 323 " (cutoff:3.500A) Processing helix chain '1' and resid 350 through 365 removed outlier: 3.933A pdb=" N TRP 1 354 " --> pdb=" O SER 1 350 " (cutoff:3.500A) Processing helix chain '1' and resid 377 through 388 removed outlier: 3.823A pdb=" N ARG 1 388 " --> pdb=" O SER 1 384 " (cutoff:3.500A) Processing helix chain '1' and resid 419 through 427 removed outlier: 3.943A pdb=" N GLY 1 427 " --> pdb=" O SER 1 423 " (cutoff:3.500A) Processing helix chain '1' and resid 436 through 443 Processing helix chain '1' and resid 461 through 467 Processing helix chain '1' and resid 471 through 497 removed outlier: 4.200A pdb=" N LEU 1 475 " --> pdb=" O GLU 1 471 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE 1 492 " --> pdb=" O ASP 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 502 through 519 Processing helix chain '1' and resid 533 through 560 removed outlier: 3.878A pdb=" N THR 1 537 " --> pdb=" O PRO 1 533 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN 1 560 " --> pdb=" O GLU 1 556 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 584 removed outlier: 6.903A pdb=" N GLU 1 576 " --> pdb=" O GLU 1 572 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE 1 577 " --> pdb=" O HIS 1 573 " (cutoff:3.500A) Processing helix chain '1' and resid 593 through 616 Processing helix chain '0' and resid 106 through 114 Processing helix chain '0' and resid 255 through 267 Processing helix chain '0' and resid 280 through 294 removed outlier: 3.643A pdb=" N MET 0 284 " --> pdb=" O ARG 0 280 " (cutoff:3.500A) Proline residue: 0 292 - end of helix Processing helix chain '0' and resid 319 through 340 removed outlier: 3.723A pdb=" N ARG 0 323 " --> pdb=" O PRO 0 319 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE 0 327 " --> pdb=" O ARG 0 323 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR 0 328 " --> pdb=" O GLU 0 324 " (cutoff:3.500A) Processing helix chain '0' and resid 350 through 365 removed outlier: 3.720A pdb=" N TRP 0 354 " --> pdb=" O SER 0 350 " (cutoff:3.500A) Processing helix chain '0' and resid 377 through 387 Processing helix chain '0' and resid 412 through 416 removed outlier: 3.781A pdb=" N ASP 0 416 " --> pdb=" O PRO 0 413 " (cutoff:3.500A) Processing helix chain '0' and resid 419 through 427 Processing helix chain '0' and resid 436 through 442 Processing helix chain '0' and resid 457 through 469 removed outlier: 4.025A pdb=" N GLU 0 463 " --> pdb=" O ARG 0 459 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR 0 464 " --> pdb=" O ALA 0 460 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS 0 467 " --> pdb=" O GLU 0 463 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS 0 468 " --> pdb=" O TYR 0 464 " (cutoff:3.500A) Processing helix chain '0' and resid 471 through 496 removed outlier: 4.042A pdb=" N LEU 0 475 " --> pdb=" O GLU 0 471 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU 0 491 " --> pdb=" O GLU 0 487 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE 0 492 " --> pdb=" O ASP 0 488 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL 0 496 " --> pdb=" O ILE 0 492 " (cutoff:3.500A) Processing helix chain '0' and resid 502 through 519 Processing helix chain '0' and resid 533 through 561 removed outlier: 3.602A pdb=" N THR 0 558 " --> pdb=" O ALA 0 554 " (cutoff:3.500A) Processing helix chain '0' and resid 566 through 583 removed outlier: 3.878A pdb=" N ILE 0 570 " --> pdb=" O THR 0 566 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU 0 576 " --> pdb=" O GLU 0 572 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE 0 577 " --> pdb=" O HIS 0 573 " (cutoff:3.500A) Processing helix chain '0' and resid 584 through 587 Processing helix chain '0' and resid 593 through 616 Processing helix chain '2' and resid 105 through 114 Processing helix chain '2' and resid 256 through 266 removed outlier: 3.571A pdb=" N SER 2 260 " --> pdb=" O LYS 2 256 " (cutoff:3.500A) Processing helix chain '2' and resid 280 through 294 removed outlier: 3.768A pdb=" N MET 2 284 " --> pdb=" O ARG 2 280 " (cutoff:3.500A) Proline residue: 2 292 - end of helix Processing helix chain '2' and resid 304 through 309 Processing helix chain '2' and resid 319 through 339 removed outlier: 4.670A pdb=" N ILE 2 327 " --> pdb=" O ARG 2 323 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR 2 328 " --> pdb=" O GLU 2 324 " (cutoff:3.500A) Processing helix chain '2' and resid 350 through 364 removed outlier: 3.996A pdb=" N ARG 2 364 " --> pdb=" O GLU 2 360 " (cutoff:3.500A) Processing helix chain '2' and resid 377 through 387 Processing helix chain '2' and resid 419 through 427 Processing helix chain '2' and resid 436 through 442 Processing helix chain '2' and resid 457 through 469 removed outlier: 4.342A pdb=" N GLU 2 463 " --> pdb=" O ARG 2 459 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR 2 464 " --> pdb=" O ALA 2 460 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS 2 468 " --> pdb=" O TYR 2 464 " (cutoff:3.500A) Processing helix chain '2' and resid 471 through 497 removed outlier: 3.503A pdb=" N LEU 2 475 " --> pdb=" O GLU 2 471 " (cutoff:3.500A) Processing helix chain '2' and resid 502 through 519 removed outlier: 4.107A pdb=" N THR 2 508 " --> pdb=" O THR 2 504 " (cutoff:3.500A) Processing helix chain '2' and resid 533 through 559 Processing helix chain '2' and resid 566 through 574 Processing helix chain '2' and resid 574 through 583 Processing helix chain '2' and resid 593 through 616 Processing helix chain '3' and resid 124 through 128 removed outlier: 3.548A pdb=" N LEU 3 128 " --> pdb=" O GLU 3 125 " (cutoff:3.500A) Processing helix chain '3' and resid 198 through 209 removed outlier: 3.936A pdb=" N ILE 3 202 " --> pdb=" O PRO 3 198 " (cutoff:3.500A) Processing helix chain '3' and resid 237 through 251 removed outlier: 3.507A pdb=" N ALA 3 241 " --> pdb=" O ASN 3 237 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN 3 251 " --> pdb=" O ASP 3 247 " (cutoff:3.500A) Processing helix chain '3' and resid 252 through 255 removed outlier: 3.952A pdb=" N ASP 3 255 " --> pdb=" O GLY 3 252 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 252 through 255' Processing helix chain '3' and resid 267 through 272 Processing helix chain '3' and resid 273 through 288 Processing helix chain '3' and resid 299 through 314 removed outlier: 3.588A pdb=" N TYR 3 303 " --> pdb=" O ASP 3 299 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG 3 314 " --> pdb=" O VAL 3 310 " (cutoff:3.500A) Processing helix chain '3' and resid 319 through 323 removed outlier: 4.157A pdb=" N GLY 3 322 " --> pdb=" O GLY 3 319 " (cutoff:3.500A) Processing helix chain '3' and resid 324 through 325 No H-bonds generated for 'chain '3' and resid 324 through 325' Processing helix chain '3' and resid 326 through 336 Processing helix chain '3' and resid 357 through 360 Processing helix chain '3' and resid 363 through 373 Processing helix chain '3' and resid 380 through 386 removed outlier: 3.607A pdb=" N HIS 3 384 " --> pdb=" O ASP 3 380 " (cutoff:3.500A) Processing helix chain '3' and resid 401 through 406 Processing helix chain '3' and resid 414 through 440 removed outlier: 3.838A pdb=" N VAL 3 438 " --> pdb=" O ALA 3 434 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY 3 440 " --> pdb=" O LYS 3 436 " (cutoff:3.500A) Processing helix chain '3' and resid 441 through 444 Processing helix chain '3' and resid 445 through 462 Processing helix chain '3' and resid 472 through 485 Processing helix chain '3' and resid 486 through 487 No H-bonds generated for 'chain '3' and resid 486 through 487' Processing helix chain '3' and resid 488 through 492 Processing helix chain '3' and resid 496 through 504 removed outlier: 3.640A pdb=" N LEU 3 500 " --> pdb=" O PRO 3 496 " (cutoff:3.500A) Processing helix chain '4' and resid 124 through 128 removed outlier: 3.518A pdb=" N MET 4 127 " --> pdb=" O SER 4 124 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU 4 128 " --> pdb=" O GLU 4 125 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 124 through 128' Processing helix chain '4' and resid 159 through 161 No H-bonds generated for 'chain '4' and resid 159 through 161' Processing helix chain '4' and resid 198 through 209 Processing helix chain '4' and resid 218 through 223 Processing helix chain '4' and resid 237 through 251 removed outlier: 3.773A pdb=" N ASN 4 251 " --> pdb=" O ASP 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 252 through 255 removed outlier: 4.198A pdb=" N ASP 4 255 " --> pdb=" O GLY 4 252 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 252 through 255' Processing helix chain '4' and resid 268 through 272 removed outlier: 3.813A pdb=" N ILE 4 272 " --> pdb=" O ILE 4 269 " (cutoff:3.500A) Processing helix chain '4' and resid 273 through 290 Processing helix chain '4' and resid 299 through 314 removed outlier: 3.633A pdb=" N TYR 4 303 " --> pdb=" O ASP 4 299 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG 4 314 " --> pdb=" O VAL 4 310 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 323 removed outlier: 3.691A pdb=" N GLY 4 322 " --> pdb=" O GLY 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 324 through 325 No H-bonds generated for 'chain '4' and resid 324 through 325' Processing helix chain '4' and resid 326 through 336 Processing helix chain '4' and resid 357 through 360 Processing helix chain '4' and resid 363 through 373 Processing helix chain '4' and resid 381 through 386 Processing helix chain '4' and resid 401 through 406 removed outlier: 3.541A pdb=" N ILE 4 406 " --> pdb=" O MET 4 402 " (cutoff:3.500A) Processing helix chain '4' and resid 415 through 440 Processing helix chain '4' and resid 441 through 444 Processing helix chain '4' and resid 445 through 462 Processing helix chain '4' and resid 472 through 485 Processing helix chain '4' and resid 496 through 504 Processing helix chain '5' and resid 124 through 128 Processing helix chain '5' and resid 159 through 163 Processing helix chain '5' and resid 174 through 179 Processing helix chain '5' and resid 198 through 209 Processing helix chain '5' and resid 213 through 217 Processing helix chain '5' and resid 219 through 224 removed outlier: 3.529A pdb=" N GLU 5 224 " --> pdb=" O ASP 5 221 " (cutoff:3.500A) Processing helix chain '5' and resid 237 through 252 Processing helix chain '5' and resid 253 through 255 No H-bonds generated for 'chain '5' and resid 253 through 255' Processing helix chain '5' and resid 267 through 272 Processing helix chain '5' and resid 273 through 288 Processing helix chain '5' and resid 299 through 315 removed outlier: 3.816A pdb=" N TYR 5 303 " --> pdb=" O ASP 5 299 " (cutoff:3.500A) Processing helix chain '5' and resid 319 through 323 Processing helix chain '5' and resid 324 through 325 No H-bonds generated for 'chain '5' and resid 324 through 325' Processing helix chain '5' and resid 326 through 336 Processing helix chain '5' and resid 357 through 360 Processing helix chain '5' and resid 363 through 371 Processing helix chain '5' and resid 380 through 386 Processing helix chain '5' and resid 401 through 406 removed outlier: 3.968A pdb=" N ILE 5 406 " --> pdb=" O MET 5 402 " (cutoff:3.500A) Processing helix chain '5' and resid 415 through 439 Processing helix chain '5' and resid 440 through 444 Processing helix chain '5' and resid 445 through 462 Processing helix chain '5' and resid 472 through 485 Processing helix chain '5' and resid 496 through 504 removed outlier: 4.431A pdb=" N GLU 5 502 " --> pdb=" O SER 5 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '7' and resid 92 through 94 Processing sheet with id=AA2, first strand: chain '7' and resid 97 through 99 Processing sheet with id=AA3, first strand: chain '8' and resid 164 through 167 removed outlier: 3.762A pdb=" N ILE 8 183 " --> pdb=" O VAL 8 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '9' and resid 131 through 135 removed outlier: 6.795A pdb=" N MET 9 132 " --> pdb=" O GLN 9 166 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '9' and resid 164 through 167 current: chain '9' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain '9' and resid 190 through 195 current: chain '0' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 28 through 32 current: chain '0' and resid 50 through 58 removed outlier: 5.748A pdb=" N ILE 0 54 " --> pdb=" O GLN 0 65 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN 0 65 " --> pdb=" O ILE 0 54 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG 0 56 " --> pdb=" O THR 0 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '0' and resid 61 through 66 current: chain '4' and resid 81 through 90 removed outlier: 5.889A pdb=" N VAL 4 86 " --> pdb=" O GLN 4 97 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN 4 97 " --> pdb=" O VAL 4 86 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU 4 88 " --> pdb=" O VAL 4 95 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '4' and resid 93 through 98 current: chain '5' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 57 through 60 current: chain '5' and resid 81 through 90 removed outlier: 5.975A pdb=" N VAL 5 86 " --> pdb=" O GLN 5 97 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN 5 97 " --> pdb=" O VAL 5 86 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU 5 88 " --> pdb=" O VAL 5 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 164 through 165 Processing sheet with id=AA6, first strand: chain '6' and resid 317 through 321 removed outlier: 4.057A pdb=" N LEU 6 6 " --> pdb=" O TYR 6 372 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR 6 372 " --> pdb=" O LEU 6 6 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER 6 8 " --> pdb=" O VAL 6 370 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL 6 370 " --> pdb=" O SER 6 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '6' and resid 182 through 185 Processing sheet with id=AA8, first strand: chain 'a' and resid 10 through 18 Processing sheet with id=AA9, first strand: chain 'a' and resid 205 through 209 removed outlier: 4.115A pdb=" N LYS a 224 " --> pdb=" O ILE a 209 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'X' and resid 36 through 38 removed outlier: 6.891A pdb=" N VAL X 10 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN X 67 " --> pdb=" O ILE X 11 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE X 64 " --> pdb=" O LEU X 89 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE X 91 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE X 66 " --> pdb=" O ILE X 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 262 through 264 removed outlier: 3.862A pdb=" N GLN c 396 " --> pdb=" O LEU c 262 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE c 363 " --> pdb=" O ILE c 395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 276 through 277 removed outlier: 3.602A pdb=" N VAL c 270 " --> pdb=" O LYS c 277 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN c 267 " --> pdb=" O HIS c 391 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS c 391 " --> pdb=" O ASN c 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 300 through 302 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 300 through 302 current: chain 'c' and resid 314 through 326 removed outlier: 3.607A pdb=" N ARG c 331 " --> pdb=" O TYR c 326 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 331 through 334 current: chain 'c' and resid 346 through 350 Processing sheet with id=AB5, first strand: chain '1' and resid 19 through 25 removed outlier: 3.748A pdb=" N TYR 1 20 " --> pdb=" O CYS 1 32 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR 1 30 " --> pdb=" O HIS 1 22 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL 1 24 " --> pdb=" O VAL 1 28 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL 1 28 " --> pdb=" O VAL 1 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 28 through 32 current: chain '1' and resid 50 through 58 removed outlier: 6.735A pdb=" N THR 1 63 " --> pdb=" O ILE 1 55 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU 1 57 " --> pdb=" O MET 1 61 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 61 through 66 current: chain '2' and resid 50 through 58 removed outlier: 5.966A pdb=" N ILE 2 54 " --> pdb=" O GLN 2 65 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN 2 65 " --> pdb=" O ILE 2 54 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG 2 56 " --> pdb=" O THR 2 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '2' and resid 61 through 66 current: chain '3' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 57 through 60 current: chain '3' and resid 81 through 90 removed outlier: 6.923A pdb=" N VAL 3 95 " --> pdb=" O LEU 3 87 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL 3 89 " --> pdb=" O LYS 3 93 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LYS 3 93 " --> pdb=" O VAL 3 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '1' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 98 through 99 current: chain '1' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 309 through 312 current: chain '1' and resid 401 through 408 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 401 through 408 current: chain '1' and resid 454 through 455 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '1' and resid 164 through 167 removed outlier: 3.785A pdb=" N GLY 1 154 " --> pdb=" O ILE 1 166 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY 1 183 " --> pdb=" O PHE 1 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '1' and resid 146 through 147 removed outlier: 3.586A pdb=" N GLY 1 174 " --> pdb=" O ILE 1 147 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU 1 195 " --> pdb=" O SER 1 175 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR 1 177 " --> pdb=" O GLU 1 193 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU 1 193 " --> pdb=" O THR 1 177 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU 1 192 " --> pdb=" O PHE 1 203 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU 1 194 " --> pdb=" O GLU 1 201 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '1' and resid 295 through 296 Processing sheet with id=AC1, first strand: chain '0' and resid 87 through 90 removed outlier: 3.814A pdb=" N TRP 0 209 " --> pdb=" O VAL 0 88 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '0' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 98 through 99 current: chain '0' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 309 through 312 current: chain '0' and resid 401 through 408 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 401 through 408 current: chain '0' and resid 454 through 455 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain '0' and resid 164 through 167 removed outlier: 3.751A pdb=" N ILE 0 166 " --> pdb=" O GLY 0 154 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY 0 154 " --> pdb=" O ILE 0 166 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY 0 183 " --> pdb=" O PHE 0 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '0' and resid 146 through 147 removed outlier: 6.547A pdb=" N GLU 0 193 " --> pdb=" O THR 0 177 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU 0 192 " --> pdb=" O PHE 0 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '0' and resid 295 through 297 Processing sheet with id=AC6, first strand: chain '2' and resid 87 through 90 removed outlier: 3.532A pdb=" N TRP 2 209 " --> pdb=" O VAL 2 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '2' and resid 98 through 99 Processing sheet with id=AC8, first strand: chain '2' and resid 164 through 167 removed outlier: 3.867A pdb=" N GLY 2 154 " --> pdb=" O ILE 2 166 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '2' and resid 146 through 147 removed outlier: 6.558A pdb=" N GLU 2 193 " --> pdb=" O THR 2 177 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE 2 179 " --> pdb=" O VAL 2 191 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL 2 191 " --> pdb=" O ILE 2 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '2' and resid 219 through 221 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 219 through 221 current: chain '2' and resid 343 through 348 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 343 through 348 current: chain '2' and resid 401 through 410 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 401 through 410 current: chain '2' and resid 454 through 455 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain '2' and resid 226 through 227 removed outlier: 4.591A pdb=" N CYS 2 240 " --> pdb=" O LEU 2 227 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AD4, first strand: chain '3' and resid 131 through 132 removed outlier: 3.644A pdb=" N LEU 3 297 " --> pdb=" O ILE 3 351 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '3' and resid 192 through 193 Processing sheet with id=AD6, first strand: chain '3' and resid 375 through 376 Processing sheet with id=AD7, first strand: chain '4' and resid 120 through 123 Processing sheet with id=AD8, first strand: chain '4' and resid 131 through 132 removed outlier: 6.528A pdb=" N ALA 4 228 " --> pdb=" O LEU 4 294 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE 4 296 " --> pdb=" O ALA 4 228 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL 4 230 " --> pdb=" O ILE 4 296 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL 4 293 " --> pdb=" O THR 4 349 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '4' and resid 163 through 164 removed outlier: 4.475A pdb=" N ARG 4 340 " --> pdb=" O ILE 4 164 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '4' and resid 170 through 171 Processing sheet with id=AE2, first strand: chain '4' and resid 191 through 193 Processing sheet with id=AE3, first strand: chain '4' and resid 375 through 376 Processing sheet with id=AE4, first strand: chain '5' and resid 120 through 123 removed outlier: 3.525A pdb=" N LEU 5 151 " --> pdb=" O THR 5 121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP 5 149 " --> pdb=" O VAL 5 123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '5' and resid 131 through 132 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 131 through 132 current: chain '5' and resid 257 through 260 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 257 through 260 current: chain '5' and resid 347 through 355 No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain '5' and resid 376 through 379 removed outlier: 3.599A pdb=" N GLN 5 376 " --> pdb=" O LEU 5 398 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR 5 378 " --> pdb=" O PRO 5 396 " (cutoff:3.500A) 3841 hydrogen bonds defined for protein. 11238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.86 Time building geometry restraints manager: 23.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16138 1.33 - 1.46: 13354 1.46 - 1.58: 36596 1.58 - 1.70: 0 1.70 - 1.82: 685 Bond restraints: 66773 Sorted by residual: bond pdb=" CA ASN 5 345 " pdb=" CB ASN 5 345 " ideal model delta sigma weight residual 1.526 1.576 -0.050 1.76e-02 3.23e+03 7.96e+00 bond pdb=" N TYR R 114 " pdb=" CA TYR R 114 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.24e-02 6.50e+03 7.77e+00 bond pdb=" N PHE i 13 " pdb=" CA PHE i 13 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.28e-02 6.10e+03 7.72e+00 bond pdb=" CA SER 2 316 " pdb=" CB SER 2 316 " ideal model delta sigma weight residual 1.530 1.484 0.046 1.69e-02 3.50e+03 7.49e+00 bond pdb=" N SER c 369 " pdb=" CA SER c 369 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.26e-02 6.30e+03 7.28e+00 ... (remaining 66768 not shown) Histogram of bond angle deviations from ideal: 92.58 - 100.90: 112 100.90 - 109.23: 4423 109.23 - 117.55: 44525 117.55 - 125.88: 40454 125.88 - 134.20: 730 Bond angle restraints: 90244 Sorted by residual: angle pdb=" N LYS c 373 " pdb=" CA LYS c 373 " pdb=" C LYS c 373 " ideal model delta sigma weight residual 110.80 98.61 12.19 2.13e+00 2.20e-01 3.27e+01 angle pdb=" N PHE 6 291 " pdb=" CA PHE 6 291 " pdb=" CB PHE 6 291 " ideal model delta sigma weight residual 110.28 118.08 -7.80 1.55e+00 4.16e-01 2.53e+01 angle pdb=" N MET l 17 " pdb=" CA MET l 17 " pdb=" CB MET l 17 " ideal model delta sigma weight residual 110.16 117.18 -7.02 1.48e+00 4.57e-01 2.25e+01 angle pdb=" N ILE 1 102 " pdb=" CA ILE 1 102 " pdb=" C ILE 1 102 " ideal model delta sigma weight residual 111.91 108.03 3.88 8.90e-01 1.26e+00 1.90e+01 angle pdb=" C LYS c 373 " pdb=" CA LYS c 373 " pdb=" CB LYS c 373 " ideal model delta sigma weight residual 110.42 118.88 -8.46 1.99e+00 2.53e-01 1.81e+01 ... (remaining 90239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 37183 17.90 - 35.80: 2589 35.80 - 53.70: 447 53.70 - 71.60: 83 71.60 - 89.50: 47 Dihedral angle restraints: 40349 sinusoidal: 16177 harmonic: 24172 Sorted by residual: dihedral pdb=" CA GLY 0 19 " pdb=" C GLY 0 19 " pdb=" N TYR 0 20 " pdb=" CA TYR 0 20 " ideal model delta harmonic sigma weight residual 180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU a 87 " pdb=" C GLU a 87 " pdb=" N VAL a 88 " pdb=" CA VAL a 88 " ideal model delta harmonic sigma weight residual -180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA SER i 11 " pdb=" C SER i 11 " pdb=" N SER i 12 " pdb=" CA SER i 12 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 40346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 8950 0.066 - 0.133: 1187 0.133 - 0.199: 83 0.199 - 0.265: 6 0.265 - 0.332: 4 Chirality restraints: 10230 Sorted by residual: chirality pdb=" CB VAL 0 79 " pdb=" CA VAL 0 79 " pdb=" CG1 VAL 0 79 " pdb=" CG2 VAL 0 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA TYR i 10 " pdb=" N TYR i 10 " pdb=" C TYR i 10 " pdb=" CB TYR i 10 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB ILE 4 351 " pdb=" CA ILE 4 351 " pdb=" CG1 ILE 4 351 " pdb=" CG2 ILE 4 351 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 10227 not shown) Planarity restraints: 11573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR i 10 " -0.047 2.00e-02 2.50e+03 2.80e-02 1.57e+01 pdb=" CG TYR i 10 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR i 10 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR i 10 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR i 10 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR i 10 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR i 10 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR i 10 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL a 88 " -0.063 5.00e-02 4.00e+02 9.67e-02 1.49e+01 pdb=" N PRO a 89 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO a 89 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO a 89 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE a 381 " -0.012 2.00e-02 2.50e+03 2.70e-02 1.28e+01 pdb=" CG PHE a 381 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE a 381 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE a 381 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE a 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE a 381 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE a 381 " -0.000 2.00e-02 2.50e+03 ... (remaining 11570 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 9514 2.76 - 3.29: 68471 3.29 - 3.83: 107415 3.83 - 4.36: 125296 4.36 - 4.90: 209156 Nonbonded interactions: 519852 Sorted by model distance: nonbonded pdb=" O LEU 2 237 " pdb=" NH2 ARG 2 476 " model vdw 2.222 2.520 nonbonded pdb=" O ASN 1 317 " pdb=" ND2 ASN 1 317 " model vdw 2.285 2.520 nonbonded pdb=" O THR 2 315 " pdb=" C SER 2 316 " model vdw 2.371 3.270 nonbonded pdb=" O ASN 1 123 " pdb=" OD1 ASN 1 123 " model vdw 2.433 3.040 nonbonded pdb=" O ALA T 76 " pdb=" OE1 GLN T 80 " model vdw 2.433 3.040 ... (remaining 519847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and resid 17 through 616) selection = chain '1' selection = chain '2' } ncs_group { reference = chain '3' selection = (chain '4' and (resid 39 through 216 or resid 224 through 506)) selection = (chain '5' and (resid 39 through 216 or resid 224 through 506)) } ncs_group { reference = chain '8' selection = chain '9' selection = chain 'Q' } ncs_group { reference = chain 'R' selection = chain 'T' selection = chain 'V' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 19.010 Check model and map are aligned: 0.370 Set scattering table: 0.460 Process input model: 135.290 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.430 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5414 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 : 0.004 0.079 66773 Z= 0.280 Angle : 0.773 12.188 90244 Z= 0.429 Chirality : 0.044 0.332 10230 Planarity : 0.006 0.128 11573 Dihedral : 12.897 89.497 24839 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 0.04 % Allowed : 0.26 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.09), residues: 8314 helix: 0.92 (0.07), residues: 4593 sheet: -1.97 (0.19), residues: 632 loop : -1.63 (0.11), residues: 3089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP U 218 HIS 0.016 0.001 HIS U 443 PHE 0.057 0.002 PHE a 381 TYR 0.057 0.002 TYR i 10 ARG 0.018 0.001 ARG g 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1796 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1793 time to evaluate : 5.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 30 ARG cc_start: 0.7542 (tmm160) cc_final: 0.6816 (tpt90) REVERT: 7 45 ARG cc_start: 0.6861 (mtt90) cc_final: 0.5173 (ptt-90) REVERT: 7 58 MET cc_start: 0.6075 (mmp) cc_final: 0.5417 (mmt) REVERT: 7 173 GLU cc_start: 0.4633 (mt-10) cc_final: 0.4300 (mt-10) REVERT: 7 203 LYS cc_start: 0.7682 (tptp) cc_final: 0.7467 (tptp) REVERT: 8 57 TYR cc_start: 0.6481 (m-10) cc_final: 0.6077 (m-10) REVERT: 8 58 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7273 (tm-30) REVERT: 8 120 VAL cc_start: 0.9015 (t) cc_final: 0.8701 (m) REVERT: 8 164 ASP cc_start: 0.6901 (t0) cc_final: 0.6643 (p0) REVERT: 8 177 ILE cc_start: 0.7660 (mp) cc_final: 0.7005 (mp) REVERT: 8 187 ASP cc_start: 0.7869 (m-30) cc_final: 0.7603 (m-30) REVERT: 9 155 TYR cc_start: 0.7576 (t80) cc_final: 0.7241 (t80) REVERT: 9 202 LEU cc_start: 0.8523 (tp) cc_final: 0.8243 (mm) REVERT: Q 16 MET cc_start: 0.2314 (mmt) cc_final: 0.1668 (mmt) REVERT: Q 36 GLU cc_start: 0.5729 (tp30) cc_final: 0.5032 (mp0) REVERT: Q 60 LYS cc_start: 0.7261 (ptmt) cc_final: 0.6746 (ptmm) REVERT: Q 70 ILE cc_start: 0.8010 (mm) cc_final: 0.7794 (mm) REVERT: Q 77 ASN cc_start: 0.8298 (m-40) cc_final: 0.8012 (t0) REVERT: Q 96 ASN cc_start: 0.7711 (m110) cc_final: 0.7425 (m110) REVERT: Q 120 VAL cc_start: 0.8824 (m) cc_final: 0.8542 (p) REVERT: Q 131 ARG cc_start: 0.7760 (mmt-90) cc_final: 0.7176 (mmm160) REVERT: Q 135 ARG cc_start: 0.8382 (ttt180) cc_final: 0.7647 (mtp180) REVERT: Q 162 ASP cc_start: 0.6762 (p0) cc_final: 0.6317 (p0) REVERT: Q 200 LEU cc_start: 0.8738 (tp) cc_final: 0.8534 (pp) REVERT: R 63 MET cc_start: 0.4241 (mtt) cc_final: 0.3545 (tpt) REVERT: R 113 ASN cc_start: 0.8503 (m-40) cc_final: 0.8223 (m-40) REVERT: T 24 ASP cc_start: 0.5679 (t0) cc_final: 0.5211 (p0) REVERT: V 47 TYR cc_start: 0.5853 (m-10) cc_final: 0.5290 (m-10) REVERT: V 56 GLN cc_start: 0.5422 (mm-40) cc_final: 0.4805 (pt0) REVERT: 6 172 LYS cc_start: 0.4395 (pttt) cc_final: 0.2633 (ttmt) REVERT: 6 257 GLU cc_start: 0.5886 (tm-30) cc_final: 0.5653 (tm-30) REVERT: 6 366 TYR cc_start: 0.3020 (m-80) cc_final: 0.1848 (m-80) REVERT: 6 370 VAL cc_start: 0.6080 (t) cc_final: 0.5688 (m) REVERT: U 162 ASN cc_start: 0.5963 (m-40) cc_final: 0.4097 (t0) REVERT: U 392 LYS cc_start: 0.4174 (mttt) cc_final: 0.2398 (tptp) REVERT: a 95 ILE cc_start: 0.4732 (mt) cc_final: 0.4524 (mt) REVERT: a 230 PHE cc_start: 0.3199 (t80) cc_final: 0.2844 (t80) REVERT: a 231 PHE cc_start: 0.4231 (m-80) cc_final: 0.2880 (m-80) REVERT: a 237 LYS cc_start: 0.5826 (mttt) cc_final: 0.5373 (mptt) REVERT: a 248 ARG cc_start: 0.3246 (mmp-170) cc_final: 0.2411 (ttm-80) REVERT: a 261 ARG cc_start: 0.4500 (ttt180) cc_final: 0.3829 (ttp80) REVERT: a 277 MET cc_start: 0.7487 (mmp) cc_final: 0.6162 (tpt) REVERT: a 385 VAL cc_start: 0.5989 (t) cc_final: 0.5671 (t) REVERT: a 446 MET cc_start: 0.5549 (mtm) cc_final: 0.5063 (mtm) REVERT: a 491 MET cc_start: 0.4345 (ttm) cc_final: 0.4109 (ttm) REVERT: a 545 MET cc_start: 0.4996 (tmm) cc_final: 0.2567 (tpt) REVERT: a 571 LYS cc_start: 0.7760 (pttt) cc_final: 0.7476 (pptt) REVERT: a 807 LEU cc_start: 0.8278 (tp) cc_final: 0.7854 (tp) REVERT: e 61 ASN cc_start: 0.3122 (m-40) cc_final: 0.2868 (m-40) REVERT: b 107 MET cc_start: 0.4285 (mmp) cc_final: 0.3577 (mmp) REVERT: b 178 ILE cc_start: 0.2890 (tt) cc_final: 0.2667 (tt) REVERT: g 44 MET cc_start: 0.6033 (mmp) cc_final: 0.5725 (mmm) REVERT: g 64 ILE cc_start: 0.6618 (mt) cc_final: 0.6395 (mt) REVERT: h 25 PHE cc_start: 0.7918 (m-10) cc_final: 0.7666 (m-80) REVERT: h 118 VAL cc_start: 0.7451 (t) cc_final: 0.7194 (t) REVERT: h 131 MET cc_start: 0.7334 (ttp) cc_final: 0.6646 (ttp) REVERT: h 137 PHE cc_start: 0.5004 (t80) cc_final: 0.4656 (t80) REVERT: h 139 GLU cc_start: 0.5445 (tp30) cc_final: 0.5174 (tp30) REVERT: h 150 LEU cc_start: 0.8062 (mt) cc_final: 0.7858 (mt) REVERT: i 14 PHE cc_start: 0.7414 (m-80) cc_final: 0.6744 (m-80) REVERT: j 23 MET cc_start: 0.7808 (mmm) cc_final: 0.6699 (tpt) REVERT: j 87 TYR cc_start: 0.4806 (m-80) cc_final: 0.3897 (t80) REVERT: k 28 MET cc_start: 0.5099 (mmt) cc_final: 0.3957 (ptm) REVERT: l 137 PHE cc_start: 0.3188 (t80) cc_final: 0.2912 (t80) REVERT: m 17 MET cc_start: 0.6483 (mtm) cc_final: 0.6268 (mtm) REVERT: m 48 ARG cc_start: 0.4808 (mmt180) cc_final: 0.4176 (mmm-85) REVERT: m 52 ILE cc_start: 0.6577 (mt) cc_final: 0.6175 (mt) REVERT: m 86 LEU cc_start: 0.1251 (tp) cc_final: 0.0731 (tp) REVERT: m 123 GLN cc_start: 0.6398 (tt0) cc_final: 0.6156 (tt0) REVERT: o 76 ILE cc_start: 0.7028 (mt) cc_final: 0.6823 (mt) REVERT: X 25 ILE cc_start: 0.8261 (pt) cc_final: 0.7780 (mp) REVERT: c 255 ASN cc_start: -0.0086 (m-40) cc_final: -0.1120 (t0) REVERT: c 298 ASP cc_start: 0.3647 (t0) cc_final: 0.3023 (t0) REVERT: c 377 LEU cc_start: 0.5290 (tp) cc_final: 0.3605 (mt) REVERT: c 429 MET cc_start: 0.4489 (mmm) cc_final: 0.3653 (mmp) REVERT: p 331 MET cc_start: 0.2663 (mmm) cc_final: 0.1924 (mmm) REVERT: 1 22 HIS cc_start: 0.7973 (t-90) cc_final: 0.7691 (t-90) REVERT: 1 194 LEU cc_start: 0.8197 (pt) cc_final: 0.7766 (pt) REVERT: 1 228 LEU cc_start: 0.8314 (tp) cc_final: 0.7581 (mm) REVERT: 1 324 GLU cc_start: 0.8113 (tt0) cc_final: 0.7579 (tt0) REVERT: 1 340 MET cc_start: 0.7694 (mtp) cc_final: 0.7374 (mtp) REVERT: 1 447 SER cc_start: 0.8104 (p) cc_final: 0.7782 (t) REVERT: 1 550 MET cc_start: 0.7779 (tpt) cc_final: 0.6126 (mtt) REVERT: 1 596 LYS cc_start: 0.7855 (tttt) cc_final: 0.7630 (tmtt) REVERT: 0 55 ILE cc_start: 0.9019 (pt) cc_final: 0.8798 (pt) REVERT: 0 77 ASP cc_start: 0.7983 (m-30) cc_final: 0.7596 (m-30) REVERT: 0 135 PHE cc_start: 0.8008 (t80) cc_final: 0.7456 (t80) REVERT: 0 232 ARG cc_start: 0.6900 (ptp-170) cc_final: 0.4805 (ttp80) REVERT: 0 438 LYS cc_start: 0.5530 (mtmt) cc_final: 0.4970 (pttp) REVERT: 2 77 ASP cc_start: 0.7613 (m-30) cc_final: 0.7343 (m-30) REVERT: 2 95 MET cc_start: 0.7736 (mmm) cc_final: 0.7534 (mmm) REVERT: 2 162 ILE cc_start: 0.8687 (mt) cc_final: 0.8414 (pt) REVERT: 2 220 LYS cc_start: 0.7415 (mtmm) cc_final: 0.6974 (mtmm) REVERT: 2 266 TYR cc_start: 0.6597 (m-80) cc_final: 0.6213 (m-80) REVERT: 2 317 ASN cc_start: 0.8716 (t0) cc_final: 0.8154 (t0) REVERT: 2 381 ARG cc_start: 0.8509 (mmp80) cc_final: 0.7965 (mmt180) REVERT: 2 462 ASP cc_start: 0.7692 (m-30) cc_final: 0.7491 (m-30) REVERT: 2 465 TYR cc_start: 0.6586 (m-80) cc_final: 0.5829 (m-80) REVERT: 2 530 ARG cc_start: 0.6042 (mtt180) cc_final: 0.4725 (mtm110) REVERT: 2 586 PHE cc_start: 0.6127 (m-80) cc_final: 0.5497 (m-10) REVERT: 3 49 THR cc_start: 0.8960 (m) cc_final: 0.8378 (p) REVERT: 3 127 MET cc_start: 0.8605 (mtp) cc_final: 0.8218 (mtp) REVERT: 3 152 ASP cc_start: 0.8463 (t0) cc_final: 0.8227 (t0) REVERT: 3 234 MET cc_start: 0.8270 (mtt) cc_final: 0.7989 (mmp) REVERT: 3 249 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7117 (tm-30) REVERT: 3 270 GLU cc_start: 0.8595 (tt0) cc_final: 0.8338 (tt0) REVERT: 3 294 LEU cc_start: 0.8958 (tp) cc_final: 0.8747 (tt) REVERT: 3 355 THR cc_start: 0.8772 (m) cc_final: 0.8159 (p) REVERT: 3 369 THR cc_start: 0.8210 (m) cc_final: 0.8007 (m) REVERT: 3 376 GLN cc_start: 0.7944 (pt0) cc_final: 0.7543 (pt0) REVERT: 3 413 LYS cc_start: 0.6483 (tptm) cc_final: 0.6279 (tptm) REVERT: 3 471 ARG cc_start: 0.4550 (ttm170) cc_final: 0.4159 (ttm170) REVERT: 3 497 GLN cc_start: 0.7796 (mt0) cc_final: 0.6824 (mm110) REVERT: 4 39 TYR cc_start: 0.7080 (p90) cc_final: 0.6249 (p90) REVERT: 4 118 ILE cc_start: 0.8496 (mm) cc_final: 0.8262 (mm) REVERT: 4 127 MET cc_start: 0.8444 (mmm) cc_final: 0.8074 (mmt) REVERT: 4 161 GLN cc_start: 0.8876 (tp40) cc_final: 0.8469 (tp-100) REVERT: 4 162 CYS cc_start: 0.8897 (m) cc_final: 0.7312 (t) REVERT: 4 170 ILE cc_start: 0.8479 (mt) cc_final: 0.8012 (pt) REVERT: 4 244 PHE cc_start: 0.8121 (m-80) cc_final: 0.7551 (m-80) REVERT: 4 300 MET cc_start: 0.8734 (mmm) cc_final: 0.8280 (mmm) REVERT: 4 308 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7328 (ttm170) REVERT: 4 318 PRO cc_start: 0.8931 (Cg_endo) cc_final: 0.8595 (Cg_exo) REVERT: 4 378 TYR cc_start: 0.6261 (t80) cc_final: 0.5770 (t80) REVERT: 4 390 PRO cc_start: 0.8855 (Cg_endo) cc_final: 0.8607 (Cg_exo) REVERT: 4 421 GLN cc_start: 0.8312 (tp40) cc_final: 0.7636 (tp-100) REVERT: 4 455 LEU cc_start: 0.7375 (mt) cc_final: 0.7078 (tt) REVERT: 5 70 GLU cc_start: 0.8252 (tt0) cc_final: 0.8008 (tt0) REVERT: 5 112 CYS cc_start: 0.8922 (t) cc_final: 0.8645 (t) REVERT: 5 127 MET cc_start: 0.8376 (mmt) cc_final: 0.7672 (mmt) REVERT: 5 162 CYS cc_start: 0.7988 (m) cc_final: 0.7067 (p) REVERT: 5 168 GLU cc_start: 0.7658 (pm20) cc_final: 0.7388 (pm20) REVERT: 5 197 LEU cc_start: 0.8475 (mt) cc_final: 0.8177 (mt) REVERT: 5 200 ASN cc_start: 0.8167 (m-40) cc_final: 0.7824 (m-40) REVERT: 5 234 MET cc_start: 0.7871 (ptp) cc_final: 0.7662 (ptp) REVERT: 5 238 MET cc_start: 0.8760 (tmm) cc_final: 0.8535 (tmm) REVERT: 5 244 PHE cc_start: 0.8697 (m-80) cc_final: 0.7844 (m-80) REVERT: 5 269 ILE cc_start: 0.9200 (mp) cc_final: 0.8888 (mp) REVERT: 5 321 ARG cc_start: 0.7992 (tpp80) cc_final: 0.7498 (tpp80) REVERT: 5 327 MET cc_start: 0.7606 (ttt) cc_final: 0.7234 (tmm) REVERT: 5 465 GLN cc_start: 0.8050 (tt0) cc_final: 0.7849 (tt0) REVERT: 5 475 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8388 (mt-10) outliers start: 3 outliers final: 1 residues processed: 1794 average time/residue: 0.6418 time to fit residues: 1970.0773 Evaluate side-chains 1472 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1471 time to evaluate : 5.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 700 optimal weight: 0.9980 chunk 629 optimal weight: 0.9990 chunk 349 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 424 optimal weight: 5.9990 chunk 336 optimal weight: 0.6980 chunk 650 optimal weight: 0.0570 chunk 251 optimal weight: 0.9990 chunk 395 optimal weight: 10.0000 chunk 484 optimal weight: 0.5980 chunk 753 optimal weight: 0.0040 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 63 GLN ** 9 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 336 HIS U 196 GLN U 240 GLN U 440 HIS a 363 GLN a 494 GLN a 575 ASN a 721 HIS ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 92 GLN n 92 GLN ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 57 ASN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS d 183 ASN 1 164 HIS 1 261 GLN ** 1 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 317 ASN 2 468 HIS ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 433 GLN ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 363 HIS 4 415 HIS ** 4 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 ASN 5 384 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5417 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 66773 Z= 0.181 Angle : 0.568 10.693 90244 Z= 0.302 Chirality : 0.041 0.303 10230 Planarity : 0.004 0.074 11573 Dihedral : 4.701 89.532 9103 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 0.07 % Allowed : 2.99 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.09), residues: 8314 helix: 1.45 (0.08), residues: 4656 sheet: -1.43 (0.20), residues: 622 loop : -1.39 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP 6 282 HIS 0.015 0.001 HIS X 33 PHE 0.029 0.002 PHE 9 18 TYR 0.055 0.001 TYR m 68 ARG 0.012 0.000 ARG Q 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1677 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1672 time to evaluate : 5.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 58 MET cc_start: 0.6079 (mmp) cc_final: 0.5704 (mmt) REVERT: 8 62 LYS cc_start: 0.8594 (tttp) cc_final: 0.7993 (mmmt) REVERT: 8 120 VAL cc_start: 0.9001 (t) cc_final: 0.8718 (m) REVERT: 8 183 ILE cc_start: 0.9084 (mt) cc_final: 0.8860 (mm) REVERT: 8 184 TYR cc_start: 0.7694 (m-80) cc_final: 0.6832 (m-80) REVERT: 8 191 LYS cc_start: 0.7976 (ptmt) cc_final: 0.7765 (ptmt) REVERT: 9 155 TYR cc_start: 0.7474 (t80) cc_final: 0.7140 (t80) REVERT: 9 187 ASP cc_start: 0.8187 (p0) cc_final: 0.7904 (p0) REVERT: 9 202 LEU cc_start: 0.8517 (tp) cc_final: 0.8224 (mm) REVERT: Q 54 MET cc_start: 0.7703 (mmm) cc_final: 0.7098 (mmm) REVERT: Q 77 ASN cc_start: 0.8207 (m-40) cc_final: 0.7666 (t0) REVERT: Q 120 VAL cc_start: 0.8858 (m) cc_final: 0.8629 (p) REVERT: Q 131 ARG cc_start: 0.7701 (mmt-90) cc_final: 0.7224 (mmm160) REVERT: Q 135 ARG cc_start: 0.8284 (ttt180) cc_final: 0.7505 (mtp180) REVERT: Q 155 TYR cc_start: 0.8684 (t80) cc_final: 0.8452 (t80) REVERT: Q 193 SER cc_start: 0.8684 (t) cc_final: 0.8392 (t) REVERT: R 63 MET cc_start: 0.3950 (mtt) cc_final: 0.3335 (tpt) REVERT: T 24 ASP cc_start: 0.5667 (t0) cc_final: 0.5165 (p0) REVERT: T 50 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6732 (mp0) REVERT: T 113 ASN cc_start: 0.8208 (m110) cc_final: 0.7782 (m110) REVERT: V 44 VAL cc_start: 0.6737 (t) cc_final: 0.6512 (t) REVERT: V 105 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6401 (tm-30) REVERT: 6 61 LEU cc_start: 0.7225 (pp) cc_final: 0.6769 (mt) REVERT: 6 172 LYS cc_start: 0.4212 (pttt) cc_final: 0.2727 (ttmt) REVERT: 6 366 TYR cc_start: 0.3247 (m-80) cc_final: 0.2234 (m-80) REVERT: U 100 MET cc_start: 0.4061 (ptt) cc_final: 0.3851 (mmp) REVERT: U 162 ASN cc_start: 0.5533 (m-40) cc_final: 0.3847 (t0) REVERT: U 392 LYS cc_start: 0.4026 (mttt) cc_final: 0.2409 (tptp) REVERT: a 88 VAL cc_start: 0.5300 (t) cc_final: 0.4517 (p) REVERT: a 237 LYS cc_start: 0.5680 (mttt) cc_final: 0.5322 (mmtm) REVERT: a 242 LYS cc_start: 0.2383 (tttt) cc_final: 0.2051 (tttt) REVERT: a 261 ARG cc_start: 0.4518 (ttt180) cc_final: 0.3904 (ttp80) REVERT: a 275 LEU cc_start: 0.5932 (mm) cc_final: 0.5496 (mt) REVERT: a 277 MET cc_start: 0.7195 (mmp) cc_final: 0.5892 (tpt) REVERT: a 298 ARG cc_start: 0.6471 (ptt90) cc_final: 0.6206 (ptt90) REVERT: a 374 THR cc_start: 0.6040 (p) cc_final: 0.5806 (p) REVERT: a 382 GLN cc_start: 0.7181 (mp10) cc_final: 0.6868 (mm-40) REVERT: a 409 LEU cc_start: 0.7195 (mt) cc_final: 0.6964 (mt) REVERT: a 446 MET cc_start: 0.5578 (mtm) cc_final: 0.5068 (mtm) REVERT: a 491 MET cc_start: 0.4467 (ttm) cc_final: 0.4239 (ttm) REVERT: a 557 LEU cc_start: 0.8122 (mt) cc_final: 0.7913 (mt) REVERT: a 571 LYS cc_start: 0.7584 (pttt) cc_final: 0.7366 (pptt) REVERT: e 61 ASN cc_start: 0.3163 (m-40) cc_final: 0.2945 (m-40) REVERT: f 57 ASN cc_start: 0.6315 (t0) cc_final: 0.6059 (t0) REVERT: b 9 LEU cc_start: 0.7575 (mt) cc_final: 0.7323 (mt) REVERT: b 107 MET cc_start: 0.4283 (mmp) cc_final: 0.4019 (mmt) REVERT: b 178 ILE cc_start: 0.2712 (tt) cc_final: 0.2500 (tt) REVERT: b 203 MET cc_start: 0.2398 (ppp) cc_final: 0.1917 (ptm) REVERT: g 44 MET cc_start: 0.6209 (mmp) cc_final: 0.5933 (mmm) REVERT: g 148 VAL cc_start: 0.4824 (t) cc_final: 0.4309 (t) REVERT: h 25 PHE cc_start: 0.7982 (m-10) cc_final: 0.7590 (m-80) REVERT: h 72 VAL cc_start: 0.7520 (t) cc_final: 0.7174 (p) REVERT: h 108 PHE cc_start: 0.5173 (m-80) cc_final: 0.4941 (m-80) REVERT: h 118 VAL cc_start: 0.7680 (t) cc_final: 0.7255 (t) REVERT: h 131 MET cc_start: 0.7692 (ttp) cc_final: 0.6913 (ttp) REVERT: h 137 PHE cc_start: 0.5044 (t80) cc_final: 0.4793 (t80) REVERT: h 139 GLU cc_start: 0.5515 (tp30) cc_final: 0.4943 (tp30) REVERT: h 146 LEU cc_start: 0.5390 (mm) cc_final: 0.5131 (mm) REVERT: h 150 LEU cc_start: 0.8063 (mt) cc_final: 0.7834 (mt) REVERT: j 6 ASN cc_start: 0.6309 (m110) cc_final: 0.6106 (m110) REVERT: j 23 MET cc_start: 0.7790 (mmm) cc_final: 0.7035 (tpt) REVERT: j 24 VAL cc_start: 0.7303 (p) cc_final: 0.6849 (p) REVERT: j 48 ARG cc_start: 0.6256 (tpt-90) cc_final: 0.5420 (tpm170) REVERT: j 52 ILE cc_start: 0.4170 (mp) cc_final: 0.3918 (mp) REVERT: j 87 TYR cc_start: 0.4680 (m-80) cc_final: 0.3901 (t80) REVERT: j 101 LEU cc_start: 0.8249 (mt) cc_final: 0.7960 (mt) REVERT: k 28 MET cc_start: 0.5034 (mmt) cc_final: 0.4051 (ptm) REVERT: k 76 ILE cc_start: 0.8008 (mt) cc_final: 0.7766 (mt) REVERT: l 17 MET cc_start: 0.5827 (mpp) cc_final: 0.5100 (mmm) REVERT: m 17 MET cc_start: 0.5677 (mtm) cc_final: 0.5377 (mtm) REVERT: m 86 LEU cc_start: 0.1409 (tp) cc_final: 0.0854 (tp) REVERT: o 76 ILE cc_start: 0.6737 (mt) cc_final: 0.6443 (mt) REVERT: o 151 ILE cc_start: 0.4847 (mm) cc_final: 0.4627 (mm) REVERT: X 25 ILE cc_start: 0.8227 (pt) cc_final: 0.7806 (mp) REVERT: d 240 LEU cc_start: 0.6266 (mt) cc_final: 0.5843 (mt) REVERT: d 323 GLU cc_start: 0.7892 (pp20) cc_final: 0.6163 (mm-30) REVERT: c 255 ASN cc_start: -0.0018 (m-40) cc_final: -0.1295 (t0) REVERT: c 377 LEU cc_start: 0.5069 (tp) cc_final: 0.3658 (mt) REVERT: c 429 MET cc_start: 0.4975 (mmm) cc_final: 0.4579 (mmp) REVERT: 1 22 HIS cc_start: 0.7872 (t-90) cc_final: 0.7618 (t-90) REVERT: 1 109 ILE cc_start: 0.8979 (mt) cc_final: 0.8778 (mm) REVERT: 1 228 LEU cc_start: 0.8346 (tp) cc_final: 0.7602 (mm) REVERT: 1 324 GLU cc_start: 0.7986 (tt0) cc_final: 0.7598 (tt0) REVERT: 1 550 MET cc_start: 0.7342 (tpt) cc_final: 0.6141 (mtt) REVERT: 1 596 LYS cc_start: 0.8015 (tttt) cc_final: 0.7761 (tmtt) REVERT: 0 20 TYR cc_start: 0.6821 (p90) cc_final: 0.6280 (p90) REVERT: 0 55 ILE cc_start: 0.8983 (pt) cc_final: 0.8690 (pt) REVERT: 0 77 ASP cc_start: 0.8081 (m-30) cc_final: 0.7662 (m-30) REVERT: 0 94 ILE cc_start: 0.8881 (tp) cc_final: 0.8576 (tp) REVERT: 0 232 ARG cc_start: 0.7317 (ptp-170) cc_final: 0.5050 (ttt180) REVERT: 0 282 ASN cc_start: 0.8501 (p0) cc_final: 0.8260 (p0) REVERT: 0 432 PHE cc_start: 0.7733 (t80) cc_final: 0.7504 (t80) REVERT: 0 438 LYS cc_start: 0.5340 (mtmt) cc_final: 0.4835 (pttp) REVERT: 0 465 TYR cc_start: 0.7014 (m-80) cc_final: 0.6735 (m-80) REVERT: 2 141 LEU cc_start: 0.6897 (tt) cc_final: 0.6685 (mp) REVERT: 2 220 LYS cc_start: 0.7462 (mtmm) cc_final: 0.7034 (mtmm) REVERT: 2 266 TYR cc_start: 0.6527 (m-80) cc_final: 0.5953 (m-80) REVERT: 2 317 ASN cc_start: 0.8700 (t0) cc_final: 0.8141 (t0) REVERT: 2 381 ARG cc_start: 0.8465 (mmp80) cc_final: 0.7999 (mmt180) REVERT: 2 530 ARG cc_start: 0.6025 (mtt180) cc_final: 0.4734 (mtm110) REVERT: 2 579 TYR cc_start: 0.7340 (t80) cc_final: 0.6942 (m-10) REVERT: 2 586 PHE cc_start: 0.6181 (m-80) cc_final: 0.5373 (m-10) REVERT: 3 118 ILE cc_start: 0.8930 (pt) cc_final: 0.8727 (pt) REVERT: 3 127 MET cc_start: 0.8666 (mtp) cc_final: 0.8456 (mtp) REVERT: 3 152 ASP cc_start: 0.8571 (t0) cc_final: 0.8322 (t0) REVERT: 3 234 MET cc_start: 0.8222 (mtt) cc_final: 0.7944 (mmp) REVERT: 3 270 GLU cc_start: 0.8606 (tt0) cc_final: 0.8379 (tt0) REVERT: 3 288 GLN cc_start: 0.7427 (mm-40) cc_final: 0.7103 (mm-40) REVERT: 3 355 THR cc_start: 0.8790 (m) cc_final: 0.8210 (p) REVERT: 3 368 LEU cc_start: 0.8960 (mt) cc_final: 0.8734 (mt) REVERT: 3 413 LYS cc_start: 0.6535 (tptm) cc_final: 0.6318 (tptm) REVERT: 3 497 GLN cc_start: 0.7797 (mt0) cc_final: 0.6891 (mm110) REVERT: 4 39 TYR cc_start: 0.7098 (p90) cc_final: 0.6251 (p90) REVERT: 4 47 TYR cc_start: 0.9000 (m-80) cc_final: 0.8733 (m-80) REVERT: 4 120 ARG cc_start: 0.7894 (mmt-90) cc_final: 0.7648 (mmt90) REVERT: 4 162 CYS cc_start: 0.8204 (m) cc_final: 0.7837 (t) REVERT: 4 308 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7281 (ttm170) REVERT: 4 318 PRO cc_start: 0.8901 (Cg_endo) cc_final: 0.8509 (Cg_exo) REVERT: 4 435 MET cc_start: 0.6184 (tmm) cc_final: 0.5653 (ppp) REVERT: 4 455 LEU cc_start: 0.7420 (mt) cc_final: 0.7088 (tt) REVERT: 4 469 GLU cc_start: 0.7587 (tp30) cc_final: 0.6979 (tp30) REVERT: 5 100 GLU cc_start: 0.8433 (mp0) cc_final: 0.7684 (tp30) REVERT: 5 112 CYS cc_start: 0.8848 (t) cc_final: 0.8620 (t) REVERT: 5 127 MET cc_start: 0.8546 (mmt) cc_final: 0.8249 (mmt) REVERT: 5 162 CYS cc_start: 0.7971 (m) cc_final: 0.7061 (p) REVERT: 5 168 GLU cc_start: 0.7531 (pm20) cc_final: 0.7227 (pm20) REVERT: 5 197 LEU cc_start: 0.8459 (mt) cc_final: 0.8172 (mt) REVERT: 5 244 PHE cc_start: 0.8684 (m-80) cc_final: 0.8019 (m-80) REVERT: 5 269 ILE cc_start: 0.9070 (mp) cc_final: 0.8730 (mp) REVERT: 5 296 ILE cc_start: 0.9071 (mt) cc_final: 0.8801 (mm) REVERT: 5 327 MET cc_start: 0.7438 (ttt) cc_final: 0.6578 (tmm) REVERT: 5 475 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8349 (mt-10) outliers start: 5 outliers final: 0 residues processed: 1674 average time/residue: 0.6074 time to fit residues: 1741.5622 Evaluate side-chains 1412 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1412 time to evaluate : 5.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 418 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 627 optimal weight: 10.0000 chunk 513 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 755 optimal weight: 2.9990 chunk 815 optimal weight: 5.9990 chunk 672 optimal weight: 3.9990 chunk 748 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 605 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** 9 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 149 GLN Q 74 ASN R 13 GLN V 35 GLN 6 134 ASN 6 286 ASN 6 336 HIS U 196 GLN ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 GLN ** a 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 722 GLN b 51 ASN ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN d 130 HIS d 183 ASN c 297 ASN c 387 GLN 1 261 GLN 0 65 GLN 3 161 GLN 3 350 GLN ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 456 GLN 4 161 GLN 4 205 GLN 4 345 ASN ** 4 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 54 ASN 5 171 GLN 5 251 ASN 5 384 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5501 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 66773 Z= 0.237 Angle : 0.591 13.596 90244 Z= 0.313 Chirality : 0.042 0.328 10230 Planarity : 0.005 0.072 11573 Dihedral : 4.658 80.393 9103 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.09), residues: 8314 helix: 1.52 (0.07), residues: 4664 sheet: -1.12 (0.21), residues: 642 loop : -1.40 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP 6 282 HIS 0.014 0.001 HIS 3 363 PHE 0.022 0.002 PHE 0 472 TYR 0.039 0.002 TYR m 68 ARG 0.008 0.001 ARG 5 471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1625 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1617 time to evaluate : 5.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 62 MET cc_start: 0.4829 (ptm) cc_final: 0.4560 (ptm) REVERT: 8 183 ILE cc_start: 0.9147 (mt) cc_final: 0.8895 (mm) REVERT: 8 184 TYR cc_start: 0.7780 (m-80) cc_final: 0.6865 (m-80) REVERT: 8 191 LYS cc_start: 0.8205 (ptmt) cc_final: 0.7927 (ptmt) REVERT: 9 155 TYR cc_start: 0.7600 (t80) cc_final: 0.7253 (t80) REVERT: 9 164 ASP cc_start: 0.7653 (t0) cc_final: 0.7141 (p0) REVERT: 9 187 ASP cc_start: 0.8148 (p0) cc_final: 0.7876 (p0) REVERT: Q 54 MET cc_start: 0.7730 (mmm) cc_final: 0.7043 (mmm) REVERT: Q 70 ILE cc_start: 0.8248 (mm) cc_final: 0.7829 (mm) REVERT: Q 77 ASN cc_start: 0.8364 (m-40) cc_final: 0.8055 (t0) REVERT: Q 120 VAL cc_start: 0.8933 (m) cc_final: 0.8730 (p) REVERT: Q 131 ARG cc_start: 0.7674 (mmt-90) cc_final: 0.7027 (mmm160) REVERT: Q 135 ARG cc_start: 0.8440 (ttt180) cc_final: 0.7752 (mtp180) REVERT: R 72 GLU cc_start: 0.8167 (pp20) cc_final: 0.7900 (pp20) REVERT: T 24 ASP cc_start: 0.5871 (t0) cc_final: 0.5329 (p0) REVERT: T 113 ASN cc_start: 0.8348 (m110) cc_final: 0.7946 (m110) REVERT: V 42 MET cc_start: 0.6014 (mmp) cc_final: 0.4924 (tmm) REVERT: V 105 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6563 (tm-30) REVERT: 6 61 LEU cc_start: 0.7056 (pp) cc_final: 0.6830 (mt) REVERT: 6 172 LYS cc_start: 0.4214 (pttt) cc_final: 0.2698 (ttmt) REVERT: 6 296 HIS cc_start: 0.4531 (t70) cc_final: 0.4078 (t-90) REVERT: 6 366 TYR cc_start: 0.3323 (m-80) cc_final: 0.2214 (m-80) REVERT: U 162 ASN cc_start: 0.5419 (m-40) cc_final: 0.4190 (t0) REVERT: U 208 MET cc_start: 0.3113 (tpp) cc_final: 0.2328 (tpp) REVERT: U 325 LYS cc_start: 0.3950 (mmpt) cc_final: 0.2265 (tptt) REVERT: U 392 LYS cc_start: 0.3685 (mttt) cc_final: 0.2241 (tptp) REVERT: U 460 MET cc_start: 0.1052 (mmm) cc_final: 0.0304 (mmm) REVERT: a 88 VAL cc_start: 0.5686 (t) cc_final: 0.5236 (p) REVERT: a 237 LYS cc_start: 0.5720 (mttt) cc_final: 0.5202 (mptt) REVERT: a 261 ARG cc_start: 0.4960 (ttt180) cc_final: 0.4173 (ttp80) REVERT: a 277 MET cc_start: 0.6791 (mmp) cc_final: 0.5544 (tpt) REVERT: a 303 LYS cc_start: 0.7288 (tptt) cc_final: 0.6516 (tptt) REVERT: a 382 GLN cc_start: 0.7193 (mp10) cc_final: 0.6975 (mm-40) REVERT: a 409 LEU cc_start: 0.7462 (mt) cc_final: 0.7201 (mt) REVERT: a 446 MET cc_start: 0.5514 (mtm) cc_final: 0.5024 (mtm) REVERT: a 556 MET cc_start: 0.7552 (ptp) cc_final: 0.6567 (mtp) REVERT: a 640 GLN cc_start: 0.6571 (tt0) cc_final: 0.6354 (tm-30) REVERT: b 9 LEU cc_start: 0.7701 (mt) cc_final: 0.7320 (mt) REVERT: b 107 MET cc_start: 0.4178 (mmp) cc_final: 0.3731 (mmp) REVERT: b 178 ILE cc_start: 0.2584 (tt) cc_final: 0.2377 (tt) REVERT: g 44 MET cc_start: 0.6124 (mmp) cc_final: 0.5782 (mmm) REVERT: g 87 TYR cc_start: 0.0731 (m-80) cc_final: -0.0208 (m-80) REVERT: g 148 VAL cc_start: 0.5302 (t) cc_final: 0.4745 (t) REVERT: h 25 PHE cc_start: 0.8034 (m-10) cc_final: 0.7633 (m-80) REVERT: h 72 VAL cc_start: 0.7535 (t) cc_final: 0.7203 (p) REVERT: h 93 LEU cc_start: 0.7442 (tp) cc_final: 0.7220 (tp) REVERT: h 123 GLN cc_start: 0.6632 (mm-40) cc_final: 0.6290 (tp40) REVERT: h 139 GLU cc_start: 0.5920 (tp30) cc_final: 0.5478 (mm-30) REVERT: h 146 LEU cc_start: 0.5526 (mm) cc_final: 0.5147 (mm) REVERT: i 151 ILE cc_start: 0.5068 (pt) cc_final: 0.4842 (pt) REVERT: j 48 ARG cc_start: 0.6248 (tpt-90) cc_final: 0.5422 (tpm170) REVERT: j 87 TYR cc_start: 0.4596 (m-80) cc_final: 0.3773 (t80) REVERT: k 28 MET cc_start: 0.5147 (mmt) cc_final: 0.4127 (ptm) REVERT: k 44 MET cc_start: 0.5782 (ttp) cc_final: 0.5530 (tmm) REVERT: k 76 ILE cc_start: 0.7966 (mt) cc_final: 0.7709 (mt) REVERT: l 17 MET cc_start: 0.5623 (mpp) cc_final: 0.4900 (mmt) REVERT: m 17 MET cc_start: 0.5702 (mtm) cc_final: 0.5399 (mtm) REVERT: m 44 MET cc_start: 0.1466 (ttt) cc_final: 0.1076 (mtp) REVERT: m 48 ARG cc_start: 0.3434 (mmt180) cc_final: 0.3127 (mmm-85) REVERT: m 84 ILE cc_start: 0.7656 (tp) cc_final: 0.7375 (tt) REVERT: m 86 LEU cc_start: 0.1250 (tp) cc_final: 0.0884 (tp) REVERT: o 76 ILE cc_start: 0.6960 (mt) cc_final: 0.6695 (mt) REVERT: o 132 ILE cc_start: 0.5543 (tt) cc_final: 0.5300 (tt) REVERT: o 151 ILE cc_start: 0.4953 (mm) cc_final: 0.4726 (mm) REVERT: d 150 LEU cc_start: 0.5134 (tt) cc_final: 0.4821 (mt) REVERT: d 208 MET cc_start: 0.4117 (mtt) cc_final: 0.3618 (mpp) REVERT: d 323 GLU cc_start: 0.7966 (pp20) cc_final: 0.6173 (mm-30) REVERT: c 377 LEU cc_start: 0.4719 (tp) cc_final: 0.4146 (mt) REVERT: p 331 MET cc_start: 0.2724 (mmm) cc_final: -0.1633 (ttt) REVERT: 1 324 GLU cc_start: 0.8209 (tt0) cc_final: 0.7834 (tt0) REVERT: 1 386 TYR cc_start: 0.7233 (m-80) cc_final: 0.6829 (m-10) REVERT: 1 548 TYR cc_start: 0.5530 (t80) cc_final: 0.4299 (t80) REVERT: 1 567 TRP cc_start: 0.7574 (t60) cc_final: 0.7161 (t60) REVERT: 1 596 LYS cc_start: 0.8059 (tttt) cc_final: 0.7755 (tmtt) REVERT: 0 20 TYR cc_start: 0.7245 (p90) cc_final: 0.6579 (p90) REVERT: 0 77 ASP cc_start: 0.8058 (m-30) cc_final: 0.7555 (m-30) REVERT: 0 89 GLU cc_start: 0.8126 (tt0) cc_final: 0.7899 (tt0) REVERT: 0 94 ILE cc_start: 0.8919 (tp) cc_final: 0.8645 (tp) REVERT: 0 232 ARG cc_start: 0.7499 (ptp-170) cc_final: 0.7096 (ttp80) REVERT: 0 279 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6749 (mt-10) REVERT: 0 283 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7801 (tm-30) REVERT: 0 293 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7348 (mt-10) REVERT: 0 298 VAL cc_start: 0.7792 (t) cc_final: 0.7554 (p) REVERT: 0 349 ASP cc_start: 0.7424 (t0) cc_final: 0.6816 (t0) REVERT: 0 432 PHE cc_start: 0.7517 (t80) cc_final: 0.7293 (t80) REVERT: 0 438 LYS cc_start: 0.5432 (mtmt) cc_final: 0.4923 (pttp) REVERT: 0 465 TYR cc_start: 0.7098 (m-80) cc_final: 0.6854 (m-80) REVERT: 2 89 GLU cc_start: 0.7220 (tt0) cc_final: 0.6926 (tt0) REVERT: 2 141 LEU cc_start: 0.6850 (tt) cc_final: 0.6627 (mp) REVERT: 2 220 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7258 (mtmm) REVERT: 2 266 TYR cc_start: 0.6743 (m-80) cc_final: 0.6257 (m-80) REVERT: 2 317 ASN cc_start: 0.8792 (t0) cc_final: 0.8267 (t0) REVERT: 2 359 ARG cc_start: 0.5861 (mtp-110) cc_final: 0.5575 (mtp-110) REVERT: 2 381 ARG cc_start: 0.8387 (mmp80) cc_final: 0.7655 (mmm160) REVERT: 2 394 CYS cc_start: 0.7940 (m) cc_final: 0.7524 (m) REVERT: 2 530 ARG cc_start: 0.5868 (mtt180) cc_final: 0.4557 (mtm110) REVERT: 2 586 PHE cc_start: 0.6281 (m-80) cc_final: 0.5390 (m-10) REVERT: 3 68 TYR cc_start: 0.8645 (t80) cc_final: 0.8356 (t80) REVERT: 3 261 LEU cc_start: 0.9129 (tp) cc_final: 0.8918 (tp) REVERT: 3 270 GLU cc_start: 0.8552 (tt0) cc_final: 0.8279 (tt0) REVERT: 3 300 MET cc_start: 0.8365 (mmm) cc_final: 0.8024 (mtp) REVERT: 3 368 LEU cc_start: 0.8935 (mt) cc_final: 0.8603 (mt) REVERT: 3 402 MET cc_start: 0.7873 (tpp) cc_final: 0.7115 (tpp) REVERT: 3 413 LYS cc_start: 0.6632 (tptm) cc_final: 0.6419 (pttt) REVERT: 3 497 GLN cc_start: 0.7625 (mt0) cc_final: 0.6805 (mm110) REVERT: 4 120 ARG cc_start: 0.7960 (mmt-90) cc_final: 0.7559 (mmt90) REVERT: 4 162 CYS cc_start: 0.8511 (m) cc_final: 0.8048 (t) REVERT: 4 169 MET cc_start: 0.8088 (tpp) cc_final: 0.7884 (tpp) REVERT: 4 318 PRO cc_start: 0.8899 (Cg_endo) cc_final: 0.8578 (Cg_exo) REVERT: 4 455 LEU cc_start: 0.7510 (mt) cc_final: 0.7190 (tt) REVERT: 5 100 GLU cc_start: 0.8358 (mp0) cc_final: 0.8066 (tp30) REVERT: 5 112 CYS cc_start: 0.8710 (t) cc_final: 0.8383 (t) REVERT: 5 127 MET cc_start: 0.8442 (mmt) cc_final: 0.8165 (mmt) REVERT: 5 168 GLU cc_start: 0.7616 (pm20) cc_final: 0.7387 (pm20) REVERT: 5 171 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7754 (pp30) REVERT: 5 197 LEU cc_start: 0.8392 (mt) cc_final: 0.8143 (mt) REVERT: 5 242 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7456 (ttt180) REVERT: 5 244 PHE cc_start: 0.8803 (m-80) cc_final: 0.7938 (m-80) REVERT: 5 321 ARG cc_start: 0.8045 (tpp80) cc_final: 0.7477 (tpp80) REVERT: 5 475 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8323 (mt-10) outliers start: 8 outliers final: 1 residues processed: 1621 average time/residue: 0.5946 time to fit residues: 1639.9645 Evaluate side-chains 1368 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1366 time to evaluate : 5.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 746 optimal weight: 3.9990 chunk 567 optimal weight: 4.9990 chunk 391 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 360 optimal weight: 6.9990 chunk 507 optimal weight: 9.9990 chunk 757 optimal weight: 4.9990 chunk 802 optimal weight: 0.0980 chunk 395 optimal weight: 1.9990 chunk 718 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN 7 206 GLN ** 9 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 GLN 6 336 HIS U 420 HIS a 397 ASN a 668 HIS a 722 GLN a 736 ASN f 57 ASN ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 92 GLN ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 HIS d 130 HIS d 183 ASN c 387 GLN 1 261 GLN 1 282 ASN ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 484 GLN ** 0 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 209 GLN ** 3 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 470 ASN ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 363 HIS ** 4 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 171 GLN ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 ASN 5 384 HIS ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 66773 Z= 0.196 Angle : 0.565 11.479 90244 Z= 0.296 Chirality : 0.041 0.293 10230 Planarity : 0.004 0.077 11573 Dihedral : 4.560 77.777 9103 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.09), residues: 8314 helix: 1.65 (0.08), residues: 4648 sheet: -1.05 (0.21), residues: 636 loop : -1.36 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP 6 282 HIS 0.021 0.001 HIS 6 336 PHE 0.023 0.002 PHE 4 284 TYR 0.039 0.002 TYR m 68 ARG 0.015 0.000 ARG 0 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1613 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1605 time to evaluate : 5.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 62 MET cc_start: 0.4898 (ptm) cc_final: 0.4598 (ptm) REVERT: 8 72 MET cc_start: 0.7861 (ppp) cc_final: 0.7251 (ppp) REVERT: 8 183 ILE cc_start: 0.9029 (mt) cc_final: 0.8789 (mm) REVERT: 8 212 ARG cc_start: 0.8081 (tpp80) cc_final: 0.7822 (tpp80) REVERT: 9 155 TYR cc_start: 0.7570 (t80) cc_final: 0.7172 (t80) REVERT: 9 187 ASP cc_start: 0.8241 (p0) cc_final: 0.7892 (p0) REVERT: 9 202 LEU cc_start: 0.8421 (tp) cc_final: 0.8213 (mm) REVERT: Q 54 MET cc_start: 0.7589 (mmm) cc_final: 0.7103 (mmm) REVERT: Q 70 ILE cc_start: 0.7940 (mm) cc_final: 0.7403 (mm) REVERT: Q 77 ASN cc_start: 0.8303 (m-40) cc_final: 0.8017 (t0) REVERT: Q 120 VAL cc_start: 0.8989 (m) cc_final: 0.8745 (p) REVERT: Q 131 ARG cc_start: 0.7652 (mmt-90) cc_final: 0.7016 (mmm160) REVERT: Q 135 ARG cc_start: 0.8385 (ttt180) cc_final: 0.7716 (mtp180) REVERT: Q 162 ASP cc_start: 0.6714 (p0) cc_final: 0.6229 (p0) REVERT: Q 194 ASN cc_start: 0.8281 (t0) cc_final: 0.8075 (t0) REVERT: T 24 ASP cc_start: 0.5772 (t0) cc_final: 0.5152 (p0) REVERT: T 113 ASN cc_start: 0.8352 (m110) cc_final: 0.7935 (m-40) REVERT: V 42 MET cc_start: 0.5871 (mmp) cc_final: 0.5419 (ptt) REVERT: V 44 VAL cc_start: 0.6812 (t) cc_final: 0.6526 (t) REVERT: V 105 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6551 (tm-30) REVERT: 6 61 LEU cc_start: 0.7088 (pp) cc_final: 0.6770 (mt) REVERT: 6 172 LYS cc_start: 0.3992 (pttt) cc_final: 0.2977 (mttt) REVERT: 6 296 HIS cc_start: 0.4373 (t70) cc_final: 0.4057 (t-90) REVERT: 6 366 TYR cc_start: 0.3537 (m-80) cc_final: 0.2316 (m-80) REVERT: U 156 MET cc_start: 0.4295 (ptm) cc_final: 0.3961 (ptm) REVERT: U 162 ASN cc_start: 0.5602 (m-40) cc_final: 0.4287 (t0) REVERT: U 208 MET cc_start: 0.3200 (tpp) cc_final: 0.2577 (tpp) REVERT: U 325 LYS cc_start: 0.3803 (mmpt) cc_final: 0.3253 (mmtt) REVERT: U 392 LYS cc_start: 0.3425 (mttt) cc_final: 0.2099 (mmmm) REVERT: U 434 LYS cc_start: 0.3291 (mtmt) cc_final: 0.2299 (tmtt) REVERT: U 460 MET cc_start: 0.1053 (mmm) cc_final: 0.0060 (mmm) REVERT: a 237 LYS cc_start: 0.5662 (mttt) cc_final: 0.5270 (mptt) REVERT: a 261 ARG cc_start: 0.5167 (ttt180) cc_final: 0.4352 (ttp80) REVERT: a 277 MET cc_start: 0.6916 (mmp) cc_final: 0.5630 (tpt) REVERT: a 372 ASN cc_start: 0.7143 (t0) cc_final: 0.6751 (t0) REVERT: a 409 LEU cc_start: 0.7489 (mt) cc_final: 0.7233 (mt) REVERT: a 446 MET cc_start: 0.5285 (mtm) cc_final: 0.4811 (mtm) REVERT: a 491 MET cc_start: 0.4149 (ttm) cc_final: 0.3524 (ttm) REVERT: a 556 MET cc_start: 0.7398 (ptp) cc_final: 0.6499 (mtp) REVERT: a 601 LYS cc_start: 0.8459 (ttpt) cc_final: 0.7697 (tppt) REVERT: b 9 LEU cc_start: 0.7646 (mt) cc_final: 0.7312 (mt) REVERT: b 107 MET cc_start: 0.4234 (mmp) cc_final: 0.3749 (mmp) REVERT: g 44 MET cc_start: 0.6075 (mmp) cc_final: 0.5773 (mmm) REVERT: g 87 TYR cc_start: 0.0815 (m-80) cc_final: -0.0294 (m-80) REVERT: g 148 VAL cc_start: 0.5186 (t) cc_final: 0.4591 (t) REVERT: g 152 LEU cc_start: 0.6648 (mm) cc_final: 0.6146 (tp) REVERT: h 72 VAL cc_start: 0.7437 (t) cc_final: 0.7101 (p) REVERT: h 139 GLU cc_start: 0.5929 (tp30) cc_final: 0.5332 (mm-30) REVERT: h 146 LEU cc_start: 0.5241 (mm) cc_final: 0.4998 (mm) REVERT: h 150 LEU cc_start: 0.8134 (mt) cc_final: 0.7892 (mt) REVERT: j 24 VAL cc_start: 0.7265 (p) cc_final: 0.6978 (p) REVERT: j 48 ARG cc_start: 0.6268 (tpt-90) cc_final: 0.5585 (tpm170) REVERT: j 52 ILE cc_start: 0.4110 (mp) cc_final: 0.3241 (mt) REVERT: j 53 MET cc_start: 0.3361 (mmt) cc_final: 0.3150 (mmt) REVERT: k 28 MET cc_start: 0.5126 (mmt) cc_final: 0.4139 (ptm) REVERT: k 71 VAL cc_start: 0.7520 (t) cc_final: 0.7290 (t) REVERT: k 76 ILE cc_start: 0.7934 (mt) cc_final: 0.7675 (mt) REVERT: l 8 PRO cc_start: 0.5622 (Cg_exo) cc_final: 0.5302 (Cg_endo) REVERT: l 17 MET cc_start: 0.5499 (mpp) cc_final: 0.5175 (mmt) REVERT: l 25 PHE cc_start: 0.6455 (m-10) cc_final: 0.6161 (m-80) REVERT: m 17 MET cc_start: 0.5783 (mtm) cc_final: 0.5532 (mtm) REVERT: m 48 ARG cc_start: 0.3328 (mmt180) cc_final: 0.2971 (mmm-85) REVERT: m 84 ILE cc_start: 0.7522 (tp) cc_final: 0.7187 (tt) REVERT: m 86 LEU cc_start: 0.1453 (tp) cc_final: 0.0880 (tp) REVERT: o 17 MET cc_start: 0.6547 (ttt) cc_final: 0.6012 (ttm) REVERT: o 76 ILE cc_start: 0.6916 (mt) cc_final: 0.6641 (mt) REVERT: o 151 ILE cc_start: 0.4940 (mm) cc_final: 0.4688 (mm) REVERT: d 138 MET cc_start: 0.2314 (mpp) cc_final: 0.2088 (mpp) REVERT: d 323 GLU cc_start: 0.7845 (pp20) cc_final: 0.6184 (mm-30) REVERT: c 268 PHE cc_start: 0.2946 (t80) cc_final: 0.2469 (t80) REVERT: p 331 MET cc_start: 0.2881 (mmm) cc_final: -0.1408 (ttt) REVERT: 1 228 LEU cc_start: 0.8307 (tp) cc_final: 0.8019 (tp) REVERT: 1 306 MET cc_start: 0.7897 (mtp) cc_final: 0.7506 (mtt) REVERT: 1 324 GLU cc_start: 0.8072 (tt0) cc_final: 0.7860 (tt0) REVERT: 1 548 TYR cc_start: 0.5357 (t80) cc_final: 0.4202 (t80) REVERT: 1 550 MET cc_start: 0.7689 (tpt) cc_final: 0.6427 (mtt) REVERT: 1 567 TRP cc_start: 0.7243 (t60) cc_final: 0.6972 (t60) REVERT: 1 596 LYS cc_start: 0.8041 (tttt) cc_final: 0.7615 (tptp) REVERT: 0 77 ASP cc_start: 0.7980 (m-30) cc_final: 0.7627 (m-30) REVERT: 0 89 GLU cc_start: 0.8093 (tt0) cc_final: 0.7882 (tt0) REVERT: 0 283 GLU cc_start: 0.7284 (tp30) cc_final: 0.7017 (mm-30) REVERT: 0 286 GLU cc_start: 0.8107 (tt0) cc_final: 0.7781 (tm-30) REVERT: 0 293 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7309 (mt-10) REVERT: 0 298 VAL cc_start: 0.7839 (t) cc_final: 0.7564 (p) REVERT: 0 349 ASP cc_start: 0.7348 (t0) cc_final: 0.6661 (t0) REVERT: 0 360 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8250 (tm-30) REVERT: 2 89 GLU cc_start: 0.7147 (tt0) cc_final: 0.6933 (tt0) REVERT: 2 104 ARG cc_start: 0.7774 (tpp-160) cc_final: 0.7295 (mtt90) REVERT: 2 266 TYR cc_start: 0.6781 (m-80) cc_final: 0.6206 (m-80) REVERT: 2 317 ASN cc_start: 0.8702 (t0) cc_final: 0.7985 (t0) REVERT: 2 381 ARG cc_start: 0.8355 (mmp80) cc_final: 0.7942 (mmt180) REVERT: 2 456 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7843 (tptt) REVERT: 2 458 MET cc_start: 0.7587 (tpt) cc_final: 0.7337 (tpt) REVERT: 2 464 TYR cc_start: 0.7572 (t80) cc_final: 0.7201 (t80) REVERT: 2 530 ARG cc_start: 0.5798 (mtt180) cc_final: 0.4413 (mtm110) REVERT: 2 586 PHE cc_start: 0.6351 (m-80) cc_final: 0.5470 (m-10) REVERT: 3 270 GLU cc_start: 0.8536 (tt0) cc_final: 0.8302 (tt0) REVERT: 3 368 LEU cc_start: 0.8863 (mt) cc_final: 0.8512 (mt) REVERT: 3 402 MET cc_start: 0.7844 (tpp) cc_final: 0.6898 (tpp) REVERT: 3 403 LYS cc_start: 0.8428 (tttp) cc_final: 0.8220 (tttt) REVERT: 3 413 LYS cc_start: 0.6694 (tptm) cc_final: 0.6488 (pttt) REVERT: 3 435 MET cc_start: 0.5127 (tmm) cc_final: 0.4747 (tmm) REVERT: 3 451 TYR cc_start: 0.5637 (m-10) cc_final: 0.5420 (m-10) REVERT: 3 462 PHE cc_start: 0.7583 (t80) cc_final: 0.7040 (t80) REVERT: 3 497 GLN cc_start: 0.7593 (mt0) cc_final: 0.6731 (mm110) REVERT: 4 106 ASP cc_start: 0.7740 (t0) cc_final: 0.7475 (m-30) REVERT: 4 120 ARG cc_start: 0.7883 (mmt-90) cc_final: 0.7491 (mmt90) REVERT: 4 162 CYS cc_start: 0.8583 (m) cc_final: 0.8114 (t) REVERT: 4 169 MET cc_start: 0.8210 (tpp) cc_final: 0.7992 (tpp) REVERT: 4 308 ARG cc_start: 0.8183 (ttp-170) cc_final: 0.7492 (ttm170) REVERT: 4 374 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7329 (mm-30) REVERT: 4 455 LEU cc_start: 0.7282 (mt) cc_final: 0.6879 (tt) REVERT: 5 54 ASN cc_start: 0.8012 (t0) cc_final: 0.7808 (t0) REVERT: 5 100 GLU cc_start: 0.8435 (mp0) cc_final: 0.8028 (tp30) REVERT: 5 112 CYS cc_start: 0.8688 (t) cc_final: 0.8352 (t) REVERT: 5 127 MET cc_start: 0.8587 (mmt) cc_final: 0.8294 (mmt) REVERT: 5 141 ARG cc_start: 0.8672 (mtt-85) cc_final: 0.8009 (ptt90) REVERT: 5 168 GLU cc_start: 0.7472 (pm20) cc_final: 0.7205 (pm20) REVERT: 5 197 LEU cc_start: 0.8349 (mt) cc_final: 0.8105 (mt) REVERT: 5 242 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7532 (ttt180) REVERT: 5 244 PHE cc_start: 0.8781 (m-80) cc_final: 0.7973 (m-80) REVERT: 5 321 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7263 (tpp80) REVERT: 5 475 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8354 (mt-10) outliers start: 8 outliers final: 0 residues processed: 1607 average time/residue: 0.6032 time to fit residues: 1649.5968 Evaluate side-chains 1371 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1371 time to evaluate : 5.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 668 optimal weight: 5.9990 chunk 455 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 597 optimal weight: 9.9990 chunk 331 optimal weight: 8.9990 chunk 684 optimal weight: 9.9990 chunk 554 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 409 optimal weight: 5.9990 chunk 720 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN 7 85 GLN ** 7 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 71 GLN ** 8 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 77 ASN ** 9 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 ASN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN 6 39 ASN 6 144 ASN ** 6 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 336 HIS ** a 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 397 ASN a 535 ASN ** a 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 644 GLN a 722 GLN e 61 ASN f 57 ASN b 51 ASN ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 78 ASN ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 78 ASN o 124 GLN X 82 GLN ** X 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS d 183 ASN ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 297 HIS ** d 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 255 ASN 1 207 GLN 1 261 GLN ** 1 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 430 GLN 1 609 GLN 0 103 GLN 0 140 ASN ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 484 GLN 3 181 ASN ** 3 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 350 GLN ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 415 HIS ** 4 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 73 HIS 5 171 GLN ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 HIS 5 415 HIS 5 461 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5669 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 66773 Z= 0.439 Angle : 0.816 15.899 90244 Z= 0.429 Chirality : 0.049 0.336 10230 Planarity : 0.006 0.070 11573 Dihedral : 5.434 69.766 9103 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.69 % Favored : 93.26 % Rotamer: Outliers : 0.16 % Allowed : 4.10 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.09), residues: 8314 helix: 0.69 (0.07), residues: 4630 sheet: -1.45 (0.20), residues: 666 loop : -1.82 (0.11), residues: 3018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP 6 282 HIS 0.011 0.002 HIS 1 164 PHE 0.059 0.003 PHE U 245 TYR 0.043 0.003 TYR i 144 ARG 0.011 0.001 ARG 5 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1535 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1524 time to evaluate : 5.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 62 MET cc_start: 0.5402 (ptm) cc_final: 0.5086 (ptm) REVERT: 8 185 ASN cc_start: 0.8384 (p0) cc_final: 0.8167 (p0) REVERT: 8 212 ARG cc_start: 0.8277 (tpp80) cc_final: 0.7915 (tpp80) REVERT: 9 104 LYS cc_start: 0.8979 (mttt) cc_final: 0.8631 (mtpt) REVERT: 9 115 LEU cc_start: 0.7815 (mt) cc_final: 0.7370 (pp) REVERT: 9 127 LEU cc_start: 0.8892 (tp) cc_final: 0.8575 (tt) REVERT: 9 155 TYR cc_start: 0.7694 (t80) cc_final: 0.7224 (t80) REVERT: 9 184 TYR cc_start: 0.8765 (m-10) cc_final: 0.8529 (m-10) REVERT: 9 187 ASP cc_start: 0.8377 (p0) cc_final: 0.7983 (p0) REVERT: 9 215 LEU cc_start: 0.8838 (tp) cc_final: 0.8458 (tp) REVERT: Q 54 MET cc_start: 0.7794 (mmm) cc_final: 0.7581 (mmm) REVERT: Q 70 ILE cc_start: 0.8138 (mm) cc_final: 0.7926 (mm) REVERT: Q 135 ARG cc_start: 0.8340 (ttt180) cc_final: 0.7613 (mtp180) REVERT: T 24 ASP cc_start: 0.5722 (t0) cc_final: 0.5238 (p0) REVERT: T 50 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6740 (mp0) REVERT: V 42 MET cc_start: 0.5867 (mmp) cc_final: 0.5547 (ptt) REVERT: V 44 VAL cc_start: 0.7126 (t) cc_final: 0.6784 (t) REVERT: 6 61 LEU cc_start: 0.7095 (pp) cc_final: 0.6404 (mt) REVERT: 6 71 LYS cc_start: 0.6268 (ttpt) cc_final: 0.4377 (ptmt) REVERT: 6 172 LYS cc_start: 0.4135 (pttt) cc_final: 0.2850 (mttt) REVERT: 6 251 PHE cc_start: 0.1291 (t80) cc_final: 0.0889 (t80) REVERT: U 156 MET cc_start: 0.4504 (ptm) cc_final: 0.3973 (ptm) REVERT: a 237 LYS cc_start: 0.5979 (mttt) cc_final: 0.5510 (mptt) REVERT: a 261 ARG cc_start: 0.5398 (ttt180) cc_final: 0.4431 (ttp80) REVERT: a 277 MET cc_start: 0.7240 (mmp) cc_final: 0.5921 (tpt) REVERT: a 372 ASN cc_start: 0.7317 (t0) cc_final: 0.6983 (t0) REVERT: a 446 MET cc_start: 0.5474 (mtm) cc_final: 0.4816 (mtm) REVERT: a 491 MET cc_start: 0.4439 (ttm) cc_final: 0.3577 (ttp) REVERT: a 556 MET cc_start: 0.7602 (ptp) cc_final: 0.6863 (mtp) REVERT: a 562 LEU cc_start: 0.5735 (mt) cc_final: 0.5481 (tt) REVERT: a 601 LYS cc_start: 0.8497 (ttpt) cc_final: 0.7580 (tppt) REVERT: a 640 GLN cc_start: 0.6748 (tt0) cc_final: 0.6463 (tm-30) REVERT: a 719 MET cc_start: 0.5285 (mmp) cc_final: 0.4680 (tmm) REVERT: a 742 ARG cc_start: 0.7209 (ptm-80) cc_final: 0.6973 (ptm160) REVERT: a 809 TRP cc_start: 0.6940 (t60) cc_final: 0.6327 (t60) REVERT: b 9 LEU cc_start: 0.7537 (mt) cc_final: 0.7186 (mt) REVERT: b 96 PHE cc_start: 0.6259 (m-80) cc_final: 0.5966 (m-80) REVERT: g 36 LYS cc_start: 0.7047 (mmmt) cc_final: 0.6780 (mmmm) REVERT: g 108 PHE cc_start: 0.7242 (t80) cc_final: 0.6839 (t80) REVERT: g 148 VAL cc_start: 0.5685 (t) cc_final: 0.5313 (t) REVERT: h 72 VAL cc_start: 0.7637 (t) cc_final: 0.7294 (p) REVERT: h 139 GLU cc_start: 0.6216 (tp30) cc_final: 0.5814 (mm-30) REVERT: h 146 LEU cc_start: 0.5316 (mm) cc_final: 0.5052 (mm) REVERT: h 150 LEU cc_start: 0.8139 (mt) cc_final: 0.7931 (mt) REVERT: i 47 MET cc_start: 0.7692 (mpp) cc_final: 0.7360 (mpp) REVERT: k 44 MET cc_start: 0.6221 (tmm) cc_final: 0.5934 (tmm) REVERT: k 76 ILE cc_start: 0.8080 (mt) cc_final: 0.7815 (mt) REVERT: l 17 MET cc_start: 0.5463 (mpp) cc_final: 0.5045 (mmt) REVERT: l 25 PHE cc_start: 0.6793 (m-10) cc_final: 0.6329 (m-80) REVERT: m 17 MET cc_start: 0.5972 (mtm) cc_final: 0.5695 (mtm) REVERT: m 84 ILE cc_start: 0.7565 (tp) cc_final: 0.7222 (tt) REVERT: o 76 ILE cc_start: 0.7085 (mt) cc_final: 0.6854 (mt) REVERT: o 151 ILE cc_start: 0.5054 (mm) cc_final: 0.4795 (mm) REVERT: d 34 LEU cc_start: 0.3673 (mt) cc_final: 0.3106 (mt) REVERT: d 225 ILE cc_start: 0.2120 (OUTLIER) cc_final: 0.1824 (mt) REVERT: d 240 LEU cc_start: 0.5679 (mt) cc_final: 0.5474 (mt) REVERT: c 429 MET cc_start: 0.4987 (mmm) cc_final: 0.4718 (mmp) REVERT: p 331 MET cc_start: 0.3218 (mmm) cc_final: -0.1265 (ttt) REVERT: 1 56 ARG cc_start: 0.7233 (ttm170) cc_final: 0.6985 (ttm170) REVERT: 1 194 LEU cc_start: 0.8491 (pt) cc_final: 0.8230 (pp) REVERT: 1 207 GLN cc_start: 0.8352 (mt0) cc_final: 0.8113 (mp-120) REVERT: 1 256 LYS cc_start: 0.5537 (mtmm) cc_final: 0.5323 (mtmm) REVERT: 1 548 TYR cc_start: 0.5335 (t80) cc_final: 0.4170 (t80) REVERT: 1 596 LYS cc_start: 0.8156 (tttt) cc_final: 0.7758 (tptp) REVERT: 0 20 TYR cc_start: 0.7105 (p90) cc_final: 0.6691 (p90) REVERT: 0 77 ASP cc_start: 0.8043 (m-30) cc_final: 0.7579 (m-30) REVERT: 0 89 GLU cc_start: 0.7779 (tt0) cc_final: 0.7492 (tt0) REVERT: 0 283 GLU cc_start: 0.8377 (tp30) cc_final: 0.7788 (mm-30) REVERT: 0 293 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7233 (mt-10) REVERT: 0 306 MET cc_start: 0.8249 (tpt) cc_final: 0.7894 (tpt) REVERT: 0 340 MET cc_start: 0.7259 (tpp) cc_final: 0.6949 (tmm) REVERT: 0 381 ARG cc_start: 0.8777 (mmt90) cc_final: 0.8535 (mmm-85) REVERT: 0 574 MET cc_start: 0.4475 (tmm) cc_final: 0.3312 (tmm) REVERT: 0 608 MET cc_start: 0.6933 (tpt) cc_final: 0.6718 (tpt) REVERT: 2 189 ASP cc_start: 0.6628 (m-30) cc_final: 0.6178 (t70) REVERT: 2 317 ASN cc_start: 0.8675 (t0) cc_final: 0.8192 (t0) REVERT: 2 394 CYS cc_start: 0.7823 (m) cc_final: 0.7543 (m) REVERT: 2 456 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7993 (tptt) REVERT: 2 488 ASP cc_start: 0.7488 (t0) cc_final: 0.7166 (m-30) REVERT: 2 530 ARG cc_start: 0.5900 (mtt180) cc_final: 0.4109 (mtm110) REVERT: 3 106 ASP cc_start: 0.8622 (t0) cc_final: 0.8258 (t0) REVERT: 3 164 ILE cc_start: 0.8270 (mt) cc_final: 0.7885 (mt) REVERT: 3 270 GLU cc_start: 0.8455 (tt0) cc_final: 0.8146 (tt0) REVERT: 3 402 MET cc_start: 0.8215 (tpp) cc_final: 0.7535 (tpp) REVERT: 3 497 GLN cc_start: 0.7648 (mt0) cc_final: 0.6884 (mm110) REVERT: 4 40 LEU cc_start: 0.8812 (tp) cc_final: 0.8297 (mm) REVERT: 4 70 GLU cc_start: 0.7868 (pt0) cc_final: 0.7401 (pt0) REVERT: 4 105 ILE cc_start: 0.8905 (mt) cc_final: 0.8590 (mm) REVERT: 4 120 ARG cc_start: 0.8211 (mmt-90) cc_final: 0.7834 (mmt90) REVERT: 4 162 CYS cc_start: 0.8680 (m) cc_final: 0.8392 (t) REVERT: 4 200 ASN cc_start: 0.8440 (m-40) cc_final: 0.8209 (m-40) REVERT: 4 335 TYR cc_start: 0.8447 (m-10) cc_final: 0.7496 (m-10) REVERT: 4 455 LEU cc_start: 0.7285 (mt) cc_final: 0.6851 (tt) REVERT: 4 492 LEU cc_start: 0.7910 (mt) cc_final: 0.7486 (mt) REVERT: 5 100 GLU cc_start: 0.8528 (mp0) cc_final: 0.8038 (tp30) REVERT: 5 127 MET cc_start: 0.8430 (mmt) cc_final: 0.7987 (mmt) REVERT: 5 159 ASN cc_start: 0.8121 (t0) cc_final: 0.7709 (t0) REVERT: 5 168 GLU cc_start: 0.7691 (pm20) cc_final: 0.7339 (pm20) REVERT: 5 201 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8218 (tp30) REVERT: 5 299 ASP cc_start: 0.7004 (t0) cc_final: 0.6553 (t0) REVERT: 5 321 ARG cc_start: 0.7611 (tpp80) cc_final: 0.7266 (tpp80) REVERT: 5 326 TYR cc_start: 0.7822 (p90) cc_final: 0.7605 (p90) REVERT: 5 328 TYR cc_start: 0.7431 (t80) cc_final: 0.7201 (t80) REVERT: 5 336 GLU cc_start: 0.7321 (pt0) cc_final: 0.6643 (pt0) REVERT: 5 350 GLN cc_start: 0.8801 (mm110) cc_final: 0.8565 (mm110) REVERT: 5 384 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.7336 (t70) outliers start: 11 outliers final: 3 residues processed: 1531 average time/residue: 0.6379 time to fit residues: 1674.9417 Evaluate side-chains 1313 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1308 time to evaluate : 5.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 269 optimal weight: 1.9990 chunk 722 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 471 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 803 optimal weight: 1.9990 chunk 666 optimal weight: 0.3980 chunk 371 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 265 optimal weight: 30.0000 chunk 421 optimal weight: 0.7980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 71 GLN 8 206 GLN ** 9 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 336 HIS U 162 ASN U 370 HIS ** U 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 397 ASN a 722 GLN f 57 ASN b 113 ASN ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 78 ASN X 33 HIS d 10 ASN d 119 GLN ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 338 GLN c 354 GLN c 387 GLN 1 261 GLN ** 1 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 415 HIS ** 4 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 171 GLN 5 205 GLN ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5579 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 66773 Z= 0.226 Angle : 0.631 15.991 90244 Z= 0.330 Chirality : 0.043 0.319 10230 Planarity : 0.005 0.104 11573 Dihedral : 5.003 70.749 9103 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 0.06 % Allowed : 1.73 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.09), residues: 8314 helix: 1.10 (0.07), residues: 4657 sheet: -1.31 (0.20), residues: 661 loop : -1.61 (0.11), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP 6 282 HIS 0.022 0.001 HIS 6 336 PHE 0.033 0.002 PHE i 90 TYR 0.046 0.002 TYR m 68 ARG 0.011 0.001 ARG 3 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1547 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1543 time to evaluate : 5.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 62 MET cc_start: 0.5253 (ptm) cc_final: 0.4889 (ptm) REVERT: 8 72 MET cc_start: 0.8097 (ppp) cc_final: 0.7498 (ppp) REVERT: 8 183 ILE cc_start: 0.9125 (mt) cc_final: 0.8888 (mm) REVERT: 8 184 TYR cc_start: 0.8170 (m-10) cc_final: 0.7774 (m-80) REVERT: 8 185 ASN cc_start: 0.8364 (p0) cc_final: 0.8149 (p0) REVERT: 9 115 LEU cc_start: 0.7574 (mt) cc_final: 0.7371 (pp) REVERT: 9 155 TYR cc_start: 0.7616 (t80) cc_final: 0.7141 (t80) REVERT: 9 187 ASP cc_start: 0.8472 (p0) cc_final: 0.8144 (p0) REVERT: 9 208 MET cc_start: 0.8474 (mmp) cc_final: 0.8133 (tpt) REVERT: Q 77 ASN cc_start: 0.8445 (m-40) cc_final: 0.8189 (t0) REVERT: Q 135 ARG cc_start: 0.8402 (ttt180) cc_final: 0.7796 (mtp180) REVERT: T 24 ASP cc_start: 0.5866 (t0) cc_final: 0.5329 (p0) REVERT: T 113 ASN cc_start: 0.8326 (m110) cc_final: 0.7958 (m-40) REVERT: V 42 MET cc_start: 0.5780 (mmp) cc_final: 0.5398 (ptt) REVERT: V 44 VAL cc_start: 0.7025 (t) cc_final: 0.6544 (t) REVERT: V 105 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6520 (tm-30) REVERT: 6 61 LEU cc_start: 0.6849 (pp) cc_final: 0.6372 (mt) REVERT: 6 71 LYS cc_start: 0.6573 (ttpt) cc_final: 0.4613 (ptmt) REVERT: 6 125 ILE cc_start: 0.3797 (mm) cc_final: 0.3517 (mm) REVERT: 6 172 LYS cc_start: 0.4012 (pttt) cc_final: 0.3037 (mttt) REVERT: 6 242 ARG cc_start: 0.5288 (ptp-170) cc_final: 0.3873 (mmm-85) REVERT: 6 296 HIS cc_start: 0.4799 (t70) cc_final: 0.4526 (t-90) REVERT: U 162 ASN cc_start: 0.4995 (m-40) cc_final: 0.4329 (t0) REVERT: U 208 MET cc_start: 0.3193 (tpp) cc_final: 0.2735 (tpp) REVERT: U 460 MET cc_start: 0.1382 (mmt) cc_final: 0.0598 (mmt) REVERT: a 237 LYS cc_start: 0.5726 (mttt) cc_final: 0.5357 (mptt) REVERT: a 261 ARG cc_start: 0.5325 (ttt180) cc_final: 0.4401 (ttp80) REVERT: a 277 MET cc_start: 0.7035 (mmp) cc_final: 0.5688 (tpt) REVERT: a 372 ASN cc_start: 0.7172 (t0) cc_final: 0.6852 (t0) REVERT: a 446 MET cc_start: 0.5544 (mtm) cc_final: 0.4952 (mtm) REVERT: a 491 MET cc_start: 0.4519 (ttm) cc_final: 0.3947 (ttp) REVERT: a 556 MET cc_start: 0.7307 (ptp) cc_final: 0.6487 (mtp) REVERT: a 601 LYS cc_start: 0.8437 (ttpt) cc_final: 0.7684 (tppt) REVERT: a 742 ARG cc_start: 0.7109 (ptm-80) cc_final: 0.6875 (ptm160) REVERT: a 822 PHE cc_start: 0.5629 (t80) cc_final: 0.5096 (t80) REVERT: b 9 LEU cc_start: 0.7327 (mt) cc_final: 0.7024 (mt) REVERT: b 178 ILE cc_start: 0.2818 (tt) cc_final: 0.2411 (tt) REVERT: g 148 VAL cc_start: 0.5164 (t) cc_final: 0.4785 (t) REVERT: h 25 PHE cc_start: 0.8283 (m-10) cc_final: 0.7942 (m-80) REVERT: h 72 VAL cc_start: 0.7540 (t) cc_final: 0.7187 (p) REVERT: h 139 GLU cc_start: 0.5746 (tp30) cc_final: 0.5400 (mm-30) REVERT: i 47 MET cc_start: 0.7770 (mpp) cc_final: 0.7480 (mpp) REVERT: j 28 MET cc_start: 0.8655 (mmm) cc_final: 0.8396 (mmm) REVERT: k 44 MET cc_start: 0.6165 (tmm) cc_final: 0.5925 (tmm) REVERT: k 76 ILE cc_start: 0.8065 (mt) cc_final: 0.7808 (mt) REVERT: l 25 PHE cc_start: 0.6486 (m-10) cc_final: 0.6269 (m-80) REVERT: m 84 ILE cc_start: 0.7455 (tp) cc_final: 0.7110 (tt) REVERT: m 86 LEU cc_start: 0.1430 (tp) cc_final: 0.0953 (tp) REVERT: o 76 ILE cc_start: 0.7031 (mt) cc_final: 0.6799 (mt) REVERT: X 82 GLN cc_start: 0.5310 (tm-30) cc_final: 0.4763 (mm-40) REVERT: d 240 LEU cc_start: 0.5781 (mt) cc_final: 0.5561 (mt) REVERT: d 323 GLU cc_start: 0.7766 (pp20) cc_final: 0.5902 (mm-30) REVERT: c 387 GLN cc_start: 0.5373 (OUTLIER) cc_final: 0.5166 (tt0) REVERT: p 331 MET cc_start: 0.3338 (mmm) cc_final: -0.1254 (ttt) REVERT: 1 56 ARG cc_start: 0.7153 (ttm170) cc_final: 0.6911 (ttm170) REVERT: 1 194 LEU cc_start: 0.8450 (pt) cc_final: 0.8171 (pp) REVERT: 1 205 MET cc_start: 0.7667 (ptp) cc_final: 0.7457 (ptp) REVERT: 1 324 GLU cc_start: 0.8289 (tt0) cc_final: 0.7839 (tt0) REVERT: 1 364 ARG cc_start: 0.7661 (ttm170) cc_final: 0.7296 (ttm170) REVERT: 1 548 TYR cc_start: 0.5369 (t80) cc_final: 0.4321 (t80) REVERT: 1 567 TRP cc_start: 0.6879 (t60) cc_final: 0.5653 (t60) REVERT: 1 571 ARG cc_start: 0.6578 (mtm110) cc_final: 0.6056 (mtm110) REVERT: 1 596 LYS cc_start: 0.7986 (tttt) cc_final: 0.7666 (tptp) REVERT: 0 20 TYR cc_start: 0.7128 (p90) cc_final: 0.6731 (p90) REVERT: 0 89 GLU cc_start: 0.7756 (tt0) cc_final: 0.7542 (tt0) REVERT: 0 293 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7264 (mt-10) REVERT: 0 306 MET cc_start: 0.8344 (tpt) cc_final: 0.8033 (tpt) REVERT: 0 574 MET cc_start: 0.4509 (tmm) cc_final: 0.3410 (tmm) REVERT: 0 608 MET cc_start: 0.7236 (tpt) cc_final: 0.7012 (tpt) REVERT: 2 104 ARG cc_start: 0.7659 (tpp-160) cc_final: 0.7400 (mtt90) REVERT: 2 317 ASN cc_start: 0.8569 (t0) cc_final: 0.8112 (t0) REVERT: 2 353 ARG cc_start: 0.8040 (mpt180) cc_final: 0.7694 (mpt180) REVERT: 2 381 ARG cc_start: 0.8302 (mmp80) cc_final: 0.7741 (mmt180) REVERT: 2 394 CYS cc_start: 0.7311 (m) cc_final: 0.6994 (m) REVERT: 2 456 LYS cc_start: 0.8522 (ttpt) cc_final: 0.7948 (tptt) REVERT: 2 464 TYR cc_start: 0.7637 (t80) cc_final: 0.7407 (t80) REVERT: 2 530 ARG cc_start: 0.5921 (mtt180) cc_final: 0.4154 (mtm110) REVERT: 2 586 PHE cc_start: 0.6518 (m-80) cc_final: 0.5554 (m-80) REVERT: 3 106 ASP cc_start: 0.8501 (t0) cc_final: 0.8162 (t70) REVERT: 3 185 ARG cc_start: 0.7568 (mtp180) cc_final: 0.7152 (mtm180) REVERT: 3 187 GLN cc_start: 0.8519 (mm-40) cc_final: 0.7681 (mm-40) REVERT: 3 270 GLU cc_start: 0.8543 (tt0) cc_final: 0.8334 (tt0) REVERT: 3 294 LEU cc_start: 0.8972 (tp) cc_final: 0.8766 (tt) REVERT: 3 368 LEU cc_start: 0.8866 (mt) cc_final: 0.8577 (mt) REVERT: 3 402 MET cc_start: 0.7793 (tpp) cc_final: 0.7038 (tpp) REVERT: 3 435 MET cc_start: 0.5292 (tmm) cc_final: 0.3560 (ttp) REVERT: 3 497 GLN cc_start: 0.7534 (mt0) cc_final: 0.6777 (mm110) REVERT: 4 40 LEU cc_start: 0.8778 (tp) cc_final: 0.8208 (mm) REVERT: 4 70 GLU cc_start: 0.7739 (pt0) cc_final: 0.7170 (pt0) REVERT: 4 106 ASP cc_start: 0.7847 (t0) cc_final: 0.7617 (m-30) REVERT: 4 137 LYS cc_start: 0.8148 (mttp) cc_final: 0.7916 (tppt) REVERT: 4 200 ASN cc_start: 0.8354 (m-40) cc_final: 0.8143 (m-40) REVERT: 4 244 PHE cc_start: 0.8099 (m-80) cc_final: 0.7842 (m-80) REVERT: 4 455 LEU cc_start: 0.7324 (mt) cc_final: 0.6944 (tt) REVERT: 5 100 GLU cc_start: 0.8548 (mp0) cc_final: 0.7955 (tp30) REVERT: 5 112 CYS cc_start: 0.8659 (t) cc_final: 0.8328 (t) REVERT: 5 127 MET cc_start: 0.8633 (mmt) cc_final: 0.8239 (mmt) REVERT: 5 171 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7778 (pp30) REVERT: 5 231 PHE cc_start: 0.7835 (t80) cc_final: 0.7400 (t80) REVERT: 5 244 PHE cc_start: 0.8817 (m-80) cc_final: 0.8282 (m-80) REVERT: 5 299 ASP cc_start: 0.6714 (t0) cc_final: 0.6393 (t0) REVERT: 5 309 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8381 (tm-30) REVERT: 5 321 ARG cc_start: 0.7650 (tpp80) cc_final: 0.6888 (tpp80) REVERT: 5 328 TYR cc_start: 0.7386 (t80) cc_final: 0.6989 (t80) REVERT: 5 475 GLU cc_start: 0.8511 (mp0) cc_final: 0.8191 (mp0) outliers start: 4 outliers final: 0 residues processed: 1546 average time/residue: 0.5977 time to fit residues: 1598.3834 Evaluate side-chains 1328 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1326 time to evaluate : 5.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 774 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 457 optimal weight: 0.1980 chunk 586 optimal weight: 0.6980 chunk 454 optimal weight: 10.0000 chunk 676 optimal weight: 5.9990 chunk 448 optimal weight: 6.9990 chunk 799 optimal weight: 1.9990 chunk 500 optimal weight: 3.9990 chunk 487 optimal weight: 0.0060 chunk 369 optimal weight: 9.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** 9 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 96 ASN ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 336 HIS ** U 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 397 ASN f 57 ASN b 51 ASN ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 130 HIS ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 164 HIS ** 1 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 181 ASN ** 3 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 363 HIS 4 415 HIS 5 171 GLN ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 HIS ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 461 ASN ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5514 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 66773 Z= 0.174 Angle : 0.588 15.122 90244 Z= 0.307 Chirality : 0.041 0.292 10230 Planarity : 0.004 0.097 11573 Dihedral : 4.676 70.259 9103 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 0.06 % Allowed : 1.26 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.09), residues: 8314 helix: 1.39 (0.08), residues: 4672 sheet: -1.11 (0.21), residues: 636 loop : -1.48 (0.11), residues: 3006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.001 TRP 6 282 HIS 0.011 0.001 HIS 3 363 PHE 0.042 0.002 PHE 9 18 TYR 0.048 0.001 TYR m 68 ARG 0.014 0.000 ARG 3 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1573 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1569 time to evaluate : 5.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 62 MET cc_start: 0.5014 (ptm) cc_final: 0.4461 (ptm) REVERT: 7 97 LYS cc_start: 0.5447 (tptp) cc_final: 0.5006 (ttpp) REVERT: 7 114 GLU cc_start: 0.3563 (mm-30) cc_final: 0.2960 (mt-10) REVERT: 8 72 MET cc_start: 0.8093 (ppp) cc_final: 0.7423 (ppp) REVERT: 8 183 ILE cc_start: 0.9084 (mt) cc_final: 0.8773 (mm) REVERT: 8 184 TYR cc_start: 0.8077 (m-10) cc_final: 0.7682 (m-80) REVERT: 8 185 ASN cc_start: 0.8314 (p0) cc_final: 0.8079 (p0) REVERT: 9 155 TYR cc_start: 0.7416 (t80) cc_final: 0.6973 (t80) REVERT: 9 187 ASP cc_start: 0.8545 (p0) cc_final: 0.8176 (p0) REVERT: Q 20 GLU cc_start: 0.3474 (tp30) cc_final: 0.2068 (mp0) REVERT: Q 135 ARG cc_start: 0.8417 (ttt180) cc_final: 0.7774 (mtp180) REVERT: T 24 ASP cc_start: 0.5770 (t0) cc_final: 0.5178 (p0) REVERT: T 84 MET cc_start: 0.7402 (mtp) cc_final: 0.6685 (mtp) REVERT: T 113 ASN cc_start: 0.8264 (m110) cc_final: 0.7813 (m-40) REVERT: V 42 MET cc_start: 0.6213 (mmp) cc_final: 0.5760 (ptt) REVERT: V 105 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6477 (tm-30) REVERT: 6 61 LEU cc_start: 0.6947 (pp) cc_final: 0.6447 (mt) REVERT: 6 71 LYS cc_start: 0.6342 (ttpt) cc_final: 0.4293 (ttpt) REVERT: 6 125 ILE cc_start: 0.3751 (mm) cc_final: 0.3413 (mm) REVERT: 6 172 LYS cc_start: 0.3790 (pttt) cc_final: 0.2977 (tttt) REVERT: 6 242 ARG cc_start: 0.5486 (ptp-170) cc_final: 0.3960 (mmm-85) REVERT: 6 265 MET cc_start: 0.3261 (tpt) cc_final: 0.2853 (tpt) REVERT: 6 324 ASN cc_start: 0.3986 (m-40) cc_final: 0.3745 (m-40) REVERT: 6 370 VAL cc_start: 0.4456 (t) cc_final: 0.4244 (t) REVERT: U 156 MET cc_start: 0.4376 (ptm) cc_final: 0.4016 (ptm) REVERT: U 208 MET cc_start: 0.3164 (tpp) cc_final: 0.2691 (tpp) REVERT: U 325 LYS cc_start: 0.3632 (mmpt) cc_final: 0.2972 (mmtt) REVERT: U 392 LYS cc_start: 0.3691 (mttt) cc_final: 0.1710 (mmmm) REVERT: U 434 LYS cc_start: 0.3056 (mtmt) cc_final: 0.2366 (tmtt) REVERT: U 460 MET cc_start: 0.1295 (mmt) cc_final: 0.0852 (mmm) REVERT: a 11 THR cc_start: 0.6142 (t) cc_final: 0.5642 (t) REVERT: a 59 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7480 (tm-30) REVERT: a 237 LYS cc_start: 0.5582 (mttt) cc_final: 0.5365 (mptt) REVERT: a 277 MET cc_start: 0.6914 (mmp) cc_final: 0.5608 (tpt) REVERT: a 331 TRP cc_start: 0.5875 (m100) cc_final: 0.3928 (m-90) REVERT: a 372 ASN cc_start: 0.7008 (t0) cc_final: 0.6719 (t0) REVERT: a 446 MET cc_start: 0.5470 (mtm) cc_final: 0.4861 (mtm) REVERT: a 491 MET cc_start: 0.4601 (ttm) cc_final: 0.4050 (ttm) REVERT: a 556 MET cc_start: 0.7374 (ptp) cc_final: 0.6392 (mtp) REVERT: a 601 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7484 (tppt) REVERT: a 616 LEU cc_start: 0.6147 (tp) cc_final: 0.4358 (mp) REVERT: a 822 PHE cc_start: 0.5563 (t80) cc_final: 0.5142 (t80) REVERT: f 11 LEU cc_start: 0.3390 (mp) cc_final: 0.2844 (mt) REVERT: b 9 LEU cc_start: 0.7539 (mt) cc_final: 0.7177 (mt) REVERT: b 178 ILE cc_start: 0.2485 (tt) cc_final: 0.2271 (tt) REVERT: g 44 MET cc_start: 0.6734 (mmp) cc_final: 0.6221 (mmm) REVERT: g 87 TYR cc_start: 0.1041 (m-80) cc_final: 0.0084 (m-80) REVERT: g 148 VAL cc_start: 0.5152 (t) cc_final: 0.4656 (t) REVERT: g 152 LEU cc_start: 0.6696 (mm) cc_final: 0.6213 (tp) REVERT: h 25 PHE cc_start: 0.8290 (m-10) cc_final: 0.7854 (m-80) REVERT: h 72 VAL cc_start: 0.7530 (t) cc_final: 0.7161 (p) REVERT: h 97 LEU cc_start: 0.8324 (mt) cc_final: 0.8123 (mt) REVERT: h 139 GLU cc_start: 0.5746 (tp30) cc_final: 0.5250 (mm-30) REVERT: h 146 LEU cc_start: 0.5420 (mm) cc_final: 0.5187 (mm) REVERT: i 47 MET cc_start: 0.7899 (mpp) cc_final: 0.7618 (mpp) REVERT: j 28 MET cc_start: 0.8580 (mmm) cc_final: 0.8369 (mmm) REVERT: k 28 MET cc_start: 0.5363 (mmt) cc_final: 0.4178 (ptm) REVERT: k 44 MET cc_start: 0.6126 (tmm) cc_final: 0.5861 (tmm) REVERT: k 71 VAL cc_start: 0.7589 (t) cc_final: 0.7311 (t) REVERT: k 76 ILE cc_start: 0.8043 (mt) cc_final: 0.7792 (mt) REVERT: l 23 MET cc_start: 0.4445 (ptm) cc_final: 0.3786 (ptt) REVERT: l 25 PHE cc_start: 0.6942 (m-10) cc_final: 0.6068 (m-80) REVERT: m 84 ILE cc_start: 0.7212 (tp) cc_final: 0.6862 (tt) REVERT: m 86 LEU cc_start: 0.1370 (tp) cc_final: 0.0825 (tp) REVERT: n 112 ILE cc_start: 0.6819 (tt) cc_final: 0.6518 (mm) REVERT: o 76 ILE cc_start: 0.6844 (mt) cc_final: 0.6566 (mt) REVERT: X 82 GLN cc_start: 0.5204 (tm-30) cc_final: 0.4767 (mm-40) REVERT: d 78 MET cc_start: 0.6113 (tpt) cc_final: 0.5864 (tpp) REVERT: d 138 MET cc_start: 0.1660 (mpp) cc_final: 0.1394 (mpp) REVERT: d 323 GLU cc_start: 0.7779 (pp20) cc_final: 0.5872 (mm-30) REVERT: c 268 PHE cc_start: 0.3367 (t80) cc_final: 0.2647 (t80) REVERT: p 331 MET cc_start: 0.3188 (mmm) cc_final: -0.1435 (ttt) REVERT: 1 324 GLU cc_start: 0.8169 (tt0) cc_final: 0.7680 (tt0) REVERT: 1 548 TYR cc_start: 0.5209 (t80) cc_final: 0.4277 (t80) REVERT: 1 550 MET cc_start: 0.7432 (tpt) cc_final: 0.6212 (mtt) REVERT: 1 567 TRP cc_start: 0.6807 (t60) cc_final: 0.5614 (t60) REVERT: 1 571 ARG cc_start: 0.6574 (mtm110) cc_final: 0.6173 (mtm110) REVERT: 0 20 TYR cc_start: 0.7077 (p90) cc_final: 0.6726 (p90) REVERT: 0 77 ASP cc_start: 0.7967 (m-30) cc_final: 0.7762 (m-30) REVERT: 0 89 GLU cc_start: 0.7723 (tt0) cc_final: 0.7520 (tt0) REVERT: 0 293 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7283 (mt-10) REVERT: 0 306 MET cc_start: 0.8168 (tpt) cc_final: 0.7798 (tpt) REVERT: 0 544 MET cc_start: 0.3726 (mmm) cc_final: 0.2803 (tmm) REVERT: 0 574 MET cc_start: 0.4632 (tmm) cc_final: 0.3349 (tmm) REVERT: 2 65 GLN cc_start: 0.6203 (tp40) cc_final: 0.5170 (tp40) REVERT: 2 104 ARG cc_start: 0.7499 (tpp-160) cc_final: 0.7234 (mtt90) REVERT: 2 381 ARG cc_start: 0.8285 (mmp80) cc_final: 0.7861 (mmt180) REVERT: 2 394 CYS cc_start: 0.7082 (m) cc_final: 0.6848 (m) REVERT: 2 456 LYS cc_start: 0.8474 (ttpt) cc_final: 0.7923 (tptt) REVERT: 2 464 TYR cc_start: 0.7707 (t80) cc_final: 0.7485 (t80) REVERT: 2 530 ARG cc_start: 0.5902 (mtt180) cc_final: 0.4141 (mtm110) REVERT: 2 584 MET cc_start: 0.6770 (mmm) cc_final: 0.6155 (mmm) REVERT: 3 45 LEU cc_start: 0.8878 (tp) cc_final: 0.8610 (tp) REVERT: 3 106 ASP cc_start: 0.8432 (t0) cc_final: 0.8179 (t70) REVERT: 3 118 ILE cc_start: 0.8928 (pt) cc_final: 0.8567 (pt) REVERT: 3 169 MET cc_start: 0.7635 (mtt) cc_final: 0.7247 (mtt) REVERT: 3 185 ARG cc_start: 0.7318 (mtp180) cc_final: 0.6552 (mtm110) REVERT: 3 187 GLN cc_start: 0.8494 (mm-40) cc_final: 0.7575 (mm-40) REVERT: 3 261 LEU cc_start: 0.8966 (tp) cc_final: 0.8748 (tp) REVERT: 3 326 TYR cc_start: 0.8248 (p90) cc_final: 0.6671 (p90) REVERT: 3 402 MET cc_start: 0.7567 (tpp) cc_final: 0.7062 (tpp) REVERT: 3 435 MET cc_start: 0.5252 (tmm) cc_final: 0.3544 (ttp) REVERT: 3 497 GLN cc_start: 0.7443 (mt0) cc_final: 0.6673 (mm110) REVERT: 4 40 LEU cc_start: 0.8663 (tp) cc_final: 0.8190 (mm) REVERT: 4 70 GLU cc_start: 0.7634 (pt0) cc_final: 0.7057 (pt0) REVERT: 4 137 LYS cc_start: 0.8270 (mttp) cc_final: 0.7884 (mmmm) REVERT: 4 169 MET cc_start: 0.8131 (tpp) cc_final: 0.7806 (tpp) REVERT: 4 170 ILE cc_start: 0.8548 (mt) cc_final: 0.8183 (tt) REVERT: 4 200 ASN cc_start: 0.8236 (m-40) cc_final: 0.7973 (m-40) REVERT: 4 201 GLU cc_start: 0.8023 (mp0) cc_final: 0.6257 (tm-30) REVERT: 4 244 PHE cc_start: 0.8048 (m-80) cc_final: 0.7792 (m-80) REVERT: 4 308 ARG cc_start: 0.8223 (ttp-170) cc_final: 0.7750 (ttm170) REVERT: 4 435 MET cc_start: 0.6557 (tmm) cc_final: 0.6019 (ppp) REVERT: 4 455 LEU cc_start: 0.7299 (mt) cc_final: 0.6912 (tt) REVERT: 5 100 GLU cc_start: 0.8544 (mp0) cc_final: 0.8000 (tp30) REVERT: 5 112 CYS cc_start: 0.8554 (t) cc_final: 0.8279 (t) REVERT: 5 127 MET cc_start: 0.8611 (mmt) cc_final: 0.8121 (mmt) REVERT: 5 231 PHE cc_start: 0.7708 (t80) cc_final: 0.7352 (t80) REVERT: 5 244 PHE cc_start: 0.8684 (m-80) cc_final: 0.8218 (m-80) REVERT: 5 309 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8290 (tm-30) REVERT: 5 321 ARG cc_start: 0.7488 (tpp80) cc_final: 0.6850 (tpp80) REVERT: 5 475 GLU cc_start: 0.8635 (mp0) cc_final: 0.8263 (mp0) outliers start: 4 outliers final: 0 residues processed: 1571 average time/residue: 0.6005 time to fit residues: 1607.9479 Evaluate side-chains 1337 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1337 time to evaluate : 5.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 494 optimal weight: 5.9990 chunk 319 optimal weight: 8.9990 chunk 477 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 157 optimal weight: 0.2980 chunk 154 optimal weight: 0.4980 chunk 508 optimal weight: 20.0000 chunk 545 optimal weight: 0.8980 chunk 395 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 628 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN 7 206 GLN ** 9 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 GLN U 162 ASN ** U 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 85 ASN ** a 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 397 ASN j 78 ASN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS d 108 ASN d 119 GLN c 354 GLN c 387 GLN 1 397 ASN ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 468 HIS 0 484 GLN ** 2 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 54 ASN 4 85 GLN 4 363 HIS 4 415 HIS 5 171 GLN ** 5 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 HIS ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5494 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 66773 Z= 0.169 Angle : 0.581 13.970 90244 Z= 0.302 Chirality : 0.041 0.288 10230 Planarity : 0.004 0.087 11573 Dihedral : 4.522 71.712 9103 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.55 % Rotamer: Outliers : 0.09 % Allowed : 0.86 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 8314 helix: 1.53 (0.08), residues: 4655 sheet: -1.00 (0.21), residues: 631 loop : -1.36 (0.11), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.001 TRP 6 282 HIS 0.008 0.001 HIS d 130 PHE 0.028 0.002 PHE c 393 TYR 0.049 0.001 TYR m 68 ARG 0.010 0.000 ARG 3 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1545 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1539 time to evaluate : 5.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 62 MET cc_start: 0.5233 (ptm) cc_final: 0.4726 (ptm) REVERT: 7 97 LYS cc_start: 0.5278 (tptp) cc_final: 0.4988 (ttpp) REVERT: 7 114 GLU cc_start: 0.3396 (mm-30) cc_final: 0.2873 (mt-10) REVERT: 8 72 MET cc_start: 0.8076 (ppp) cc_final: 0.7351 (ppp) REVERT: 8 78 GLN cc_start: 0.8941 (mp10) cc_final: 0.8728 (mp10) REVERT: 8 183 ILE cc_start: 0.8988 (mt) cc_final: 0.8713 (mm) REVERT: 8 184 TYR cc_start: 0.8125 (m-10) cc_final: 0.7728 (m-80) REVERT: 8 185 ASN cc_start: 0.8326 (p0) cc_final: 0.8084 (p0) REVERT: 9 115 LEU cc_start: 0.7568 (mt) cc_final: 0.7333 (tp) REVERT: 9 155 TYR cc_start: 0.7415 (t80) cc_final: 0.7002 (t80) REVERT: 9 156 LYS cc_start: 0.7515 (tptp) cc_final: 0.7296 (tptp) REVERT: 9 187 ASP cc_start: 0.8429 (p0) cc_final: 0.8017 (p0) REVERT: Q 16 MET cc_start: 0.1695 (mmt) cc_final: 0.1176 (mmt) REVERT: Q 135 ARG cc_start: 0.8406 (ttt180) cc_final: 0.7833 (mtp180) REVERT: T 24 ASP cc_start: 0.5630 (t0) cc_final: 0.5056 (p0) REVERT: T 50 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6698 (tp30) REVERT: T 84 MET cc_start: 0.7419 (mtp) cc_final: 0.6705 (mtp) REVERT: T 113 ASN cc_start: 0.8293 (m110) cc_final: 0.8027 (m-40) REVERT: V 105 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6476 (tm-30) REVERT: 6 61 LEU cc_start: 0.6968 (pp) cc_final: 0.6488 (mt) REVERT: 6 71 LYS cc_start: 0.6084 (ttpt) cc_final: 0.5471 (ptmt) REVERT: 6 172 LYS cc_start: 0.3838 (pttt) cc_final: 0.2955 (tttt) REVERT: 6 242 ARG cc_start: 0.5449 (ptp-170) cc_final: 0.4049 (mmm-85) REVERT: 6 265 MET cc_start: 0.3067 (tpt) cc_final: 0.2634 (tpt) REVERT: U 156 MET cc_start: 0.4451 (ptm) cc_final: 0.4062 (ptm) REVERT: U 208 MET cc_start: 0.3097 (tpp) cc_final: 0.2680 (tpp) REVERT: U 434 LYS cc_start: 0.3051 (mtmt) cc_final: 0.2016 (tmtt) REVERT: U 460 MET cc_start: 0.1220 (mmt) cc_final: 0.0360 (mmt) REVERT: a 11 THR cc_start: 0.5974 (t) cc_final: 0.5715 (t) REVERT: a 59 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7468 (tm-30) REVERT: a 237 LYS cc_start: 0.5651 (mttt) cc_final: 0.5423 (mptt) REVERT: a 261 ARG cc_start: 0.4742 (ttt90) cc_final: 0.4313 (ttp80) REVERT: a 277 MET cc_start: 0.6906 (mmp) cc_final: 0.5675 (tpt) REVERT: a 331 TRP cc_start: 0.5838 (m100) cc_final: 0.3927 (m-90) REVERT: a 372 ASN cc_start: 0.6938 (t0) cc_final: 0.6574 (t0) REVERT: a 446 MET cc_start: 0.5334 (mtm) cc_final: 0.4736 (mtm) REVERT: a 491 MET cc_start: 0.4422 (ttm) cc_final: 0.3812 (ttm) REVERT: a 556 MET cc_start: 0.7366 (ptp) cc_final: 0.6426 (mtp) REVERT: a 616 LEU cc_start: 0.5778 (tp) cc_final: 0.4759 (mp) REVERT: a 809 TRP cc_start: 0.6789 (t60) cc_final: 0.6120 (t60) REVERT: a 822 PHE cc_start: 0.5779 (t80) cc_final: 0.5217 (t80) REVERT: f 11 LEU cc_start: 0.3535 (mp) cc_final: 0.2937 (mt) REVERT: b 9 LEU cc_start: 0.7350 (mt) cc_final: 0.7014 (mt) REVERT: b 178 ILE cc_start: 0.2540 (tt) cc_final: 0.2313 (tt) REVERT: g 44 MET cc_start: 0.6668 (mmp) cc_final: 0.5594 (mmm) REVERT: g 108 PHE cc_start: 0.7102 (t80) cc_final: 0.6811 (t80) REVERT: g 148 VAL cc_start: 0.5076 (t) cc_final: 0.4516 (t) REVERT: g 152 LEU cc_start: 0.6673 (mm) cc_final: 0.6181 (tp) REVERT: h 25 PHE cc_start: 0.8319 (m-10) cc_final: 0.7940 (m-80) REVERT: h 72 VAL cc_start: 0.7453 (t) cc_final: 0.7078 (p) REVERT: h 139 GLU cc_start: 0.5743 (tp30) cc_final: 0.5271 (mm-30) REVERT: h 146 LEU cc_start: 0.5241 (mm) cc_final: 0.5014 (mm) REVERT: h 150 LEU cc_start: 0.8149 (mt) cc_final: 0.7941 (mt) REVERT: i 14 PHE cc_start: 0.7047 (m-80) cc_final: 0.6184 (m-80) REVERT: i 47 MET cc_start: 0.7847 (mpp) cc_final: 0.7530 (mpp) REVERT: j 44 MET cc_start: 0.4714 (mtt) cc_final: 0.4404 (mtm) REVERT: k 28 MET cc_start: 0.5246 (mmt) cc_final: 0.4119 (ptm) REVERT: k 71 VAL cc_start: 0.7582 (t) cc_final: 0.7297 (t) REVERT: k 76 ILE cc_start: 0.8006 (mt) cc_final: 0.7770 (mt) REVERT: l 25 PHE cc_start: 0.6823 (m-10) cc_final: 0.6035 (m-80) REVERT: m 17 MET cc_start: 0.5742 (mtm) cc_final: 0.5506 (mtm) REVERT: m 84 ILE cc_start: 0.7151 (tp) cc_final: 0.6812 (tt) REVERT: m 86 LEU cc_start: 0.1027 (tp) cc_final: 0.0683 (tp) REVERT: n 112 ILE cc_start: 0.6806 (tt) cc_final: 0.6542 (mm) REVERT: o 44 MET cc_start: 0.5164 (mmm) cc_final: 0.4938 (mmm) REVERT: o 76 ILE cc_start: 0.6809 (mt) cc_final: 0.6485 (mt) REVERT: o 127 LEU cc_start: 0.6977 (mt) cc_final: 0.6634 (mt) REVERT: X 82 GLN cc_start: 0.5086 (tm-30) cc_final: 0.4640 (mm-40) REVERT: d 138 MET cc_start: 0.1465 (mpp) cc_final: 0.1225 (mpp) REVERT: d 240 LEU cc_start: 0.5688 (mt) cc_final: 0.5381 (mt) REVERT: d 323 GLU cc_start: 0.7743 (pp20) cc_final: 0.5937 (mm-30) REVERT: c 268 PHE cc_start: 0.3132 (t80) cc_final: 0.2604 (t80) REVERT: c 377 LEU cc_start: 0.5346 (tp) cc_final: 0.4464 (mt) REVERT: 1 22 HIS cc_start: 0.7768 (t-90) cc_final: 0.7516 (t-90) REVERT: 1 324 GLU cc_start: 0.8056 (tt0) cc_final: 0.7657 (tt0) REVERT: 1 346 MET cc_start: 0.8465 (ttt) cc_final: 0.8193 (ttt) REVERT: 1 548 TYR cc_start: 0.5194 (t80) cc_final: 0.4749 (t80) REVERT: 1 567 TRP cc_start: 0.6837 (t60) cc_final: 0.5484 (t60) REVERT: 1 571 ARG cc_start: 0.6588 (mtm110) cc_final: 0.6192 (mtm110) REVERT: 1 596 LYS cc_start: 0.8078 (tttt) cc_final: 0.7592 (tptp) REVERT: 0 20 TYR cc_start: 0.7013 (p90) cc_final: 0.6700 (p90) REVERT: 0 287 VAL cc_start: 0.8791 (p) cc_final: 0.8384 (p) REVERT: 0 293 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7340 (mt-10) REVERT: 0 349 ASP cc_start: 0.7508 (t0) cc_final: 0.7190 (t70) REVERT: 0 360 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8226 (tm-30) REVERT: 0 544 MET cc_start: 0.3974 (mmm) cc_final: 0.2655 (tmm) REVERT: 2 65 GLN cc_start: 0.6203 (tp40) cc_final: 0.5166 (tp40) REVERT: 2 104 ARG cc_start: 0.7527 (tpp-160) cc_final: 0.7202 (mtt90) REVERT: 2 263 LEU cc_start: 0.9000 (mt) cc_final: 0.8754 (mt) REVERT: 2 381 ARG cc_start: 0.8076 (mmp80) cc_final: 0.7842 (mmt180) REVERT: 2 456 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7861 (tptt) REVERT: 2 530 ARG cc_start: 0.5776 (mtt180) cc_final: 0.4098 (mtm110) REVERT: 2 584 MET cc_start: 0.6611 (mmm) cc_final: 0.6020 (mmm) REVERT: 2 586 PHE cc_start: 0.6601 (m-10) cc_final: 0.6372 (m-80) REVERT: 3 45 LEU cc_start: 0.8887 (tp) cc_final: 0.8526 (tp) REVERT: 3 106 ASP cc_start: 0.8386 (t0) cc_final: 0.8088 (t70) REVERT: 3 118 ILE cc_start: 0.8964 (pt) cc_final: 0.8649 (pt) REVERT: 3 174 ILE cc_start: 0.6421 (mm) cc_final: 0.6050 (mm) REVERT: 3 185 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6502 (mtm110) REVERT: 3 187 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7585 (mm-40) REVERT: 3 326 TYR cc_start: 0.8137 (p90) cc_final: 0.6612 (p90) REVERT: 3 402 MET cc_start: 0.7368 (tpp) cc_final: 0.7060 (tpp) REVERT: 3 497 GLN cc_start: 0.7470 (mt0) cc_final: 0.6667 (mm110) REVERT: 4 40 LEU cc_start: 0.8697 (tp) cc_final: 0.8195 (mm) REVERT: 4 70 GLU cc_start: 0.7634 (pt0) cc_final: 0.7091 (pt0) REVERT: 4 106 ASP cc_start: 0.8000 (t0) cc_final: 0.7715 (m-30) REVERT: 4 170 ILE cc_start: 0.8496 (mt) cc_final: 0.8108 (tt) REVERT: 4 244 PHE cc_start: 0.8065 (m-80) cc_final: 0.7799 (m-80) REVERT: 4 308 ARG cc_start: 0.8184 (ttp-170) cc_final: 0.7601 (ttm170) REVERT: 4 410 MET cc_start: 0.5751 (tpp) cc_final: 0.5249 (tpp) REVERT: 4 455 LEU cc_start: 0.7241 (mt) cc_final: 0.6750 (tt) REVERT: 4 491 MET cc_start: 0.6336 (mmp) cc_final: 0.5944 (tpp) REVERT: 5 100 GLU cc_start: 0.8615 (mp0) cc_final: 0.8192 (tp30) REVERT: 5 127 MET cc_start: 0.8613 (mmt) cc_final: 0.8348 (mmt) REVERT: 5 244 PHE cc_start: 0.8659 (m-80) cc_final: 0.8209 (m-80) REVERT: 5 309 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8283 (tm-30) REVERT: 5 321 ARG cc_start: 0.7461 (tpp80) cc_final: 0.6815 (tpp80) REVERT: 5 475 GLU cc_start: 0.8654 (mp0) cc_final: 0.8262 (mp0) outliers start: 6 outliers final: 0 residues processed: 1542 average time/residue: 0.6085 time to fit residues: 1611.2691 Evaluate side-chains 1317 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1317 time to evaluate : 5.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 727 optimal weight: 0.9990 chunk 766 optimal weight: 0.8980 chunk 699 optimal weight: 0.8980 chunk 745 optimal weight: 2.9990 chunk 448 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 585 optimal weight: 0.0170 chunk 228 optimal weight: 5.9990 chunk 673 optimal weight: 0.6980 chunk 705 optimal weight: 1.9990 chunk 742 optimal weight: 4.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** 9 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 GLN ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 336 HIS ** U 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 85 ASN ** a 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 397 ASN b 51 ASN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 387 GLN 1 397 ASN ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 468 HIS ** 2 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 54 ASN ** 4 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 171 GLN ** 5 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 HIS ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5481 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 66773 Z= 0.169 Angle : 0.586 13.832 90244 Z= 0.304 Chirality : 0.041 0.274 10230 Planarity : 0.004 0.073 11573 Dihedral : 4.453 72.261 9103 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 0.09 % Allowed : 0.50 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 8314 helix: 1.58 (0.08), residues: 4655 sheet: -0.83 (0.22), residues: 626 loop : -1.27 (0.12), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.001 TRP 6 282 HIS 0.008 0.001 HIS d 130 PHE 0.041 0.002 PHE b 96 TYR 0.043 0.001 TYR i 144 ARG 0.009 0.000 ARG 4 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1506 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1500 time to evaluate : 5.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 62 MET cc_start: 0.5297 (ptm) cc_final: 0.4718 (ptm) REVERT: 7 97 LYS cc_start: 0.5202 (tptp) cc_final: 0.4917 (ttpp) REVERT: 8 72 MET cc_start: 0.8079 (ppp) cc_final: 0.7464 (ppp) REVERT: 8 78 GLN cc_start: 0.8945 (mp10) cc_final: 0.8623 (mp10) REVERT: 8 183 ILE cc_start: 0.8975 (mt) cc_final: 0.8694 (mm) REVERT: 8 184 TYR cc_start: 0.8131 (m-10) cc_final: 0.7713 (m-80) REVERT: 8 185 ASN cc_start: 0.8306 (p0) cc_final: 0.8024 (p0) REVERT: 9 16 MET cc_start: 0.4820 (mpp) cc_final: 0.4539 (mpp) REVERT: 9 115 LEU cc_start: 0.7662 (mt) cc_final: 0.7429 (tp) REVERT: 9 124 LEU cc_start: 0.9208 (mt) cc_final: 0.8984 (mt) REVERT: 9 155 TYR cc_start: 0.7362 (t80) cc_final: 0.6966 (t80) REVERT: 9 156 LYS cc_start: 0.7511 (tptp) cc_final: 0.7298 (tptp) REVERT: 9 187 ASP cc_start: 0.8418 (p0) cc_final: 0.8028 (p0) REVERT: Q 16 MET cc_start: 0.1522 (mmt) cc_final: 0.0456 (mmt) REVERT: Q 20 GLU cc_start: 0.3629 (tp30) cc_final: 0.2181 (mp0) REVERT: Q 70 ILE cc_start: 0.8289 (mt) cc_final: 0.7984 (mm) REVERT: Q 135 ARG cc_start: 0.8460 (ttt180) cc_final: 0.8163 (mtp180) REVERT: T 24 ASP cc_start: 0.5550 (t0) cc_final: 0.4967 (p0) REVERT: T 84 MET cc_start: 0.7384 (mtp) cc_final: 0.6672 (mtp) REVERT: T 113 ASN cc_start: 0.8285 (m110) cc_final: 0.8068 (t0) REVERT: V 105 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6481 (tm-30) REVERT: 6 61 LEU cc_start: 0.7015 (pp) cc_final: 0.6480 (mt) REVERT: 6 71 LYS cc_start: 0.6370 (ttpt) cc_final: 0.5897 (ptmt) REVERT: 6 89 GLU cc_start: 0.3266 (tp30) cc_final: 0.2753 (tp30) REVERT: 6 172 LYS cc_start: 0.3879 (pttt) cc_final: 0.3052 (tttt) REVERT: 6 242 ARG cc_start: 0.5552 (ptp-170) cc_final: 0.4167 (mmm-85) REVERT: 6 265 MET cc_start: 0.3136 (tpt) cc_final: 0.2688 (tpt) REVERT: 6 336 HIS cc_start: 0.3416 (OUTLIER) cc_final: 0.3203 (m-70) REVERT: 6 370 VAL cc_start: 0.4357 (t) cc_final: 0.4128 (t) REVERT: U 156 MET cc_start: 0.4510 (ptm) cc_final: 0.4104 (ptm) REVERT: U 208 MET cc_start: 0.3063 (tpp) cc_final: 0.2582 (tpp) REVERT: U 325 LYS cc_start: 0.3732 (mmpt) cc_final: 0.3283 (mmtt) REVERT: U 392 LYS cc_start: 0.4069 (mttt) cc_final: 0.1974 (mmmm) REVERT: U 434 LYS cc_start: 0.2835 (mtmt) cc_final: 0.2069 (tmtt) REVERT: U 460 MET cc_start: 0.1145 (mmt) cc_final: -0.0000 (mmt) REVERT: a 11 THR cc_start: 0.6023 (t) cc_final: 0.5742 (t) REVERT: a 59 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7497 (tm-30) REVERT: a 237 LYS cc_start: 0.5691 (mttt) cc_final: 0.5348 (mptt) REVERT: a 261 ARG cc_start: 0.4708 (ttt90) cc_final: 0.4328 (ttp80) REVERT: a 331 TRP cc_start: 0.5904 (m100) cc_final: 0.4030 (m-90) REVERT: a 372 ASN cc_start: 0.6821 (t0) cc_final: 0.6559 (t0) REVERT: a 446 MET cc_start: 0.5331 (mtm) cc_final: 0.4718 (mtm) REVERT: a 491 MET cc_start: 0.4500 (ttm) cc_final: 0.4108 (ttm) REVERT: a 556 MET cc_start: 0.7398 (ptp) cc_final: 0.6417 (mtp) REVERT: a 616 LEU cc_start: 0.5696 (tp) cc_final: 0.4688 (mp) REVERT: a 822 PHE cc_start: 0.5629 (t80) cc_final: 0.5330 (t80) REVERT: f 11 LEU cc_start: 0.3590 (mp) cc_final: 0.2988 (mt) REVERT: b 9 LEU cc_start: 0.7432 (mt) cc_final: 0.7052 (mt) REVERT: g 36 LYS cc_start: 0.7220 (mmtt) cc_final: 0.6976 (mmtp) REVERT: g 44 MET cc_start: 0.6509 (mmp) cc_final: 0.5483 (mmm) REVERT: g 108 PHE cc_start: 0.7039 (t80) cc_final: 0.6713 (t80) REVERT: g 118 VAL cc_start: 0.5747 (t) cc_final: 0.5543 (t) REVERT: g 148 VAL cc_start: 0.4989 (t) cc_final: 0.4505 (t) REVERT: g 152 LEU cc_start: 0.6625 (mm) cc_final: 0.6133 (tp) REVERT: h 25 PHE cc_start: 0.8274 (m-10) cc_final: 0.7880 (m-80) REVERT: h 72 VAL cc_start: 0.7452 (t) cc_final: 0.7046 (p) REVERT: h 97 LEU cc_start: 0.8409 (mt) cc_final: 0.8197 (mt) REVERT: h 118 VAL cc_start: 0.7774 (t) cc_final: 0.7531 (t) REVERT: h 139 GLU cc_start: 0.5770 (tp30) cc_final: 0.5229 (mm-30) REVERT: h 146 LEU cc_start: 0.5208 (mm) cc_final: 0.4987 (mm) REVERT: i 14 PHE cc_start: 0.7106 (m-80) cc_final: 0.6209 (m-80) REVERT: i 47 MET cc_start: 0.7807 (mpp) cc_final: 0.7502 (mpp) REVERT: k 28 MET cc_start: 0.5299 (mmt) cc_final: 0.4129 (ptm) REVERT: k 44 MET cc_start: 0.5953 (tmm) cc_final: 0.5535 (tmm) REVERT: k 71 VAL cc_start: 0.7578 (t) cc_final: 0.7271 (t) REVERT: k 76 ILE cc_start: 0.7998 (mt) cc_final: 0.7737 (mt) REVERT: k 104 LEU cc_start: 0.7004 (tp) cc_final: 0.6618 (tp) REVERT: l 25 PHE cc_start: 0.6836 (m-10) cc_final: 0.6063 (m-80) REVERT: m 17 MET cc_start: 0.5792 (mtm) cc_final: 0.5549 (mtm) REVERT: m 84 ILE cc_start: 0.7149 (tp) cc_final: 0.6843 (tt) REVERT: m 86 LEU cc_start: 0.1237 (tp) cc_final: 0.0685 (tp) REVERT: n 85 THR cc_start: 0.2276 (p) cc_final: 0.1480 (m) REVERT: n 112 ILE cc_start: 0.6838 (tt) cc_final: 0.6583 (mm) REVERT: o 44 MET cc_start: 0.5352 (mmm) cc_final: 0.4901 (mmm) REVERT: o 76 ILE cc_start: 0.6876 (mt) cc_final: 0.6597 (mt) REVERT: X 82 GLN cc_start: 0.4981 (tm-30) cc_final: 0.4632 (mm-40) REVERT: d 114 THR cc_start: 0.4248 (m) cc_final: 0.4026 (p) REVERT: d 138 MET cc_start: 0.1665 (mpp) cc_final: 0.1382 (mpp) REVERT: d 240 LEU cc_start: 0.5740 (mt) cc_final: 0.5539 (mt) REVERT: d 323 GLU cc_start: 0.7753 (pp20) cc_final: 0.5836 (mm-30) REVERT: c 268 PHE cc_start: 0.2891 (t80) cc_final: 0.2408 (t80) REVERT: c 377 LEU cc_start: 0.5338 (tp) cc_final: 0.4430 (mt) REVERT: p 331 MET cc_start: 0.2738 (mmm) cc_final: -0.1972 (ttt) REVERT: 1 22 HIS cc_start: 0.7661 (t-90) cc_final: 0.7459 (t-90) REVERT: 1 205 MET cc_start: 0.7467 (ptp) cc_final: 0.7260 (ptp) REVERT: 1 324 GLU cc_start: 0.8031 (tt0) cc_final: 0.7623 (tt0) REVERT: 1 340 MET cc_start: 0.7229 (ttp) cc_final: 0.6537 (ttt) REVERT: 1 346 MET cc_start: 0.8479 (ttt) cc_final: 0.8207 (ttt) REVERT: 1 356 GLU cc_start: 0.8012 (tp30) cc_final: 0.7681 (tp30) REVERT: 1 548 TYR cc_start: 0.5179 (t80) cc_final: 0.4763 (t80) REVERT: 1 550 MET cc_start: 0.7622 (tpt) cc_final: 0.6353 (mtt) REVERT: 1 567 TRP cc_start: 0.6860 (t60) cc_final: 0.5541 (t60) REVERT: 1 571 ARG cc_start: 0.6598 (mtm110) cc_final: 0.6224 (mtm110) REVERT: 1 592 ASP cc_start: 0.7329 (m-30) cc_final: 0.7079 (m-30) REVERT: 1 596 LYS cc_start: 0.8118 (tttt) cc_final: 0.7698 (tmtt) REVERT: 0 20 TYR cc_start: 0.6969 (p90) cc_final: 0.6675 (p90) REVERT: 0 293 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7324 (mt-10) REVERT: 0 335 GLU cc_start: 0.7895 (tt0) cc_final: 0.7448 (tt0) REVERT: 0 345 SER cc_start: 0.8594 (p) cc_final: 0.8363 (p) REVERT: 0 360 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8286 (tm-30) REVERT: 0 537 THR cc_start: 0.7528 (m) cc_final: 0.7272 (m) REVERT: 0 544 MET cc_start: 0.3860 (mmm) cc_final: 0.2548 (tmm) REVERT: 0 574 MET cc_start: 0.4118 (tmm) cc_final: 0.2742 (tmm) REVERT: 2 65 GLN cc_start: 0.6120 (tp40) cc_final: 0.5175 (tp40) REVERT: 2 263 LEU cc_start: 0.8938 (mt) cc_final: 0.8708 (mt) REVERT: 2 381 ARG cc_start: 0.8244 (mmp80) cc_final: 0.7864 (mmt180) REVERT: 2 456 LYS cc_start: 0.8355 (ttpt) cc_final: 0.7839 (tptt) REVERT: 2 530 ARG cc_start: 0.5783 (mtt180) cc_final: 0.4124 (mtm110) REVERT: 2 540 MET cc_start: 0.4042 (mtm) cc_final: 0.3584 (mtm) REVERT: 2 584 MET cc_start: 0.6584 (mmm) cc_final: 0.6107 (mmm) REVERT: 3 45 LEU cc_start: 0.8880 (tp) cc_final: 0.8511 (tp) REVERT: 3 106 ASP cc_start: 0.8317 (t0) cc_final: 0.8091 (t70) REVERT: 3 118 ILE cc_start: 0.8971 (pt) cc_final: 0.8719 (pt) REVERT: 3 174 ILE cc_start: 0.6410 (mm) cc_final: 0.6034 (mm) REVERT: 3 187 GLN cc_start: 0.8571 (mm-40) cc_final: 0.7650 (mm-40) REVERT: 3 326 TYR cc_start: 0.8152 (p90) cc_final: 0.6646 (p90) REVERT: 3 402 MET cc_start: 0.7219 (tpp) cc_final: 0.6927 (tpp) REVERT: 3 497 GLN cc_start: 0.7416 (mt0) cc_final: 0.6629 (mm110) REVERT: 4 40 LEU cc_start: 0.8718 (tp) cc_final: 0.8200 (mm) REVERT: 4 70 GLU cc_start: 0.7688 (pt0) cc_final: 0.7136 (pt0) REVERT: 4 106 ASP cc_start: 0.7973 (t0) cc_final: 0.7737 (m-30) REVERT: 4 167 GLU cc_start: 0.7483 (tp30) cc_final: 0.7107 (mt-10) REVERT: 4 170 ILE cc_start: 0.8390 (mt) cc_final: 0.8116 (tt) REVERT: 4 244 PHE cc_start: 0.8110 (m-80) cc_final: 0.7876 (m-80) REVERT: 4 308 ARG cc_start: 0.8092 (ttp-170) cc_final: 0.7724 (ttm170) REVERT: 4 435 MET cc_start: 0.7023 (ppp) cc_final: 0.6335 (ppp) REVERT: 4 455 LEU cc_start: 0.7099 (mt) cc_final: 0.6625 (tt) REVERT: 4 493 LYS cc_start: 0.6510 (mppt) cc_final: 0.5676 (mmtt) REVERT: 5 100 GLU cc_start: 0.8604 (mp0) cc_final: 0.8158 (tp30) REVERT: 5 112 CYS cc_start: 0.8539 (t) cc_final: 0.8180 (t) REVERT: 5 127 MET cc_start: 0.8619 (mmt) cc_final: 0.8370 (mmt) REVERT: 5 170 ILE cc_start: 0.8747 (mp) cc_final: 0.8545 (mp) REVERT: 5 171 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7061 (pm20) REVERT: 5 244 PHE cc_start: 0.8628 (m-80) cc_final: 0.8197 (m-80) REVERT: 5 308 ARG cc_start: 0.7960 (ttp-170) cc_final: 0.6996 (ttm170) REVERT: 5 309 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8269 (tm-30) REVERT: 5 321 ARG cc_start: 0.7249 (tpp80) cc_final: 0.6769 (tpp80) outliers start: 6 outliers final: 2 residues processed: 1503 average time/residue: 0.5988 time to fit residues: 1538.5648 Evaluate side-chains 1316 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1312 time to evaluate : 5.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 489 optimal weight: 2.9990 chunk 788 optimal weight: 4.9990 chunk 481 optimal weight: 1.9990 chunk 373 optimal weight: 3.9990 chunk 548 optimal weight: 4.9990 chunk 826 optimal weight: 6.9990 chunk 761 optimal weight: 0.7980 chunk 658 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 508 optimal weight: 9.9990 chunk 403 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 162 ASN U 320 ASN ** U 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 397 ASN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS d 13 ASN d 108 ASN d 324 GLN ** c 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 172 ASN ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 468 HIS ** 2 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 350 GLN ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 HIS ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5544 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 66773 Z= 0.230 Angle : 0.630 12.088 90244 Z= 0.329 Chirality : 0.043 0.346 10230 Planarity : 0.004 0.068 11573 Dihedral : 4.607 69.600 9103 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.42 % Favored : 94.54 % Rotamer: Outliers : 0.04 % Allowed : 0.27 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.09), residues: 8314 helix: 1.44 (0.08), residues: 4665 sheet: -0.85 (0.21), residues: 641 loop : -1.38 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.002 TRP 6 282 HIS 0.008 0.001 HIS U 443 PHE 0.030 0.002 PHE b 96 TYR 0.055 0.002 TYR m 68 ARG 0.010 0.001 ARG 5 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1493 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1490 time to evaluate : 5.419 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: 7 62 MET cc_start: 0.5327 (ptm) cc_final: 0.4972 (ptm) REVERT: 7 97 LYS cc_start: 0.5233 (tptp) cc_final: 0.4937 (ttpp) REVERT: 7 114 GLU cc_start: 0.1840 (mp0) cc_final: 0.1557 (tt0) REVERT: 8 72 MET cc_start: 0.8073 (ppp) cc_final: 0.7507 (ppp) REVERT: 8 183 ILE cc_start: 0.9106 (mt) cc_final: 0.8791 (mm) REVERT: 8 184 TYR cc_start: 0.8188 (m-10) cc_final: 0.7738 (m-80) REVERT: 8 185 ASN cc_start: 0.8391 (p0) cc_final: 0.8127 (p0) REVERT: 9 115 LEU cc_start: 0.7675 (mt) cc_final: 0.7123 (pp) REVERT: 9 124 LEU cc_start: 0.9235 (mt) cc_final: 0.9000 (mt) REVERT: 9 155 TYR cc_start: 0.7462 (t80) cc_final: 0.7015 (t80) REVERT: 9 187 ASP cc_start: 0.8439 (p0) cc_final: 0.8022 (p0) REVERT: Q 20 GLU cc_start: 0.3420 (tp30) cc_final: 0.2206 (mp0) REVERT: Q 135 ARG cc_start: 0.8350 (ttt180) cc_final: 0.8090 (mtp180) REVERT: T 24 ASP cc_start: 0.5526 (t0) cc_final: 0.4955 (p0) REVERT: T 84 MET cc_start: 0.7399 (mtp) cc_final: 0.6682 (mtp) REVERT: V 105 GLU cc_start: 0.6865 (tm-30) cc_final: 0.6566 (tm-30) REVERT: 6 61 LEU cc_start: 0.6938 (pp) cc_final: 0.6263 (mt) REVERT: 6 89 GLU cc_start: 0.3438 (tp30) cc_final: 0.3008 (tp30) REVERT: 6 172 LYS cc_start: 0.3961 (pttt) cc_final: 0.2953 (tttt) REVERT: 6 265 MET cc_start: 0.3087 (tpt) cc_final: 0.2703 (tpt) REVERT: U 156 MET cc_start: 0.4468 (ptm) cc_final: 0.3874 (ptm) REVERT: U 208 MET cc_start: 0.3251 (tpp) cc_final: 0.2798 (tpp) REVERT: U 428 ILE cc_start: 0.6493 (tp) cc_final: 0.5953 (tt) REVERT: U 434 LYS cc_start: 0.3098 (mtmt) cc_final: 0.1922 (tmtt) REVERT: U 460 MET cc_start: 0.1354 (mmt) cc_final: 0.0193 (mmt) REVERT: a 11 THR cc_start: 0.6000 (t) cc_final: 0.5644 (t) REVERT: a 59 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7503 (tm-30) REVERT: a 237 LYS cc_start: 0.5654 (mttt) cc_final: 0.5410 (mptt) REVERT: a 261 ARG cc_start: 0.5169 (ttt90) cc_final: 0.4527 (ttp80) REVERT: a 331 TRP cc_start: 0.5895 (m100) cc_final: 0.4004 (m-90) REVERT: a 372 ASN cc_start: 0.6964 (t0) cc_final: 0.6704 (t0) REVERT: a 446 MET cc_start: 0.5419 (mtm) cc_final: 0.4809 (mtm) REVERT: a 491 MET cc_start: 0.4370 (ttm) cc_final: 0.3691 (ttm) REVERT: a 556 MET cc_start: 0.7670 (ptp) cc_final: 0.6730 (mtp) REVERT: a 809 TRP cc_start: 0.6915 (t60) cc_final: 0.6668 (t60) REVERT: a 822 PHE cc_start: 0.5787 (t80) cc_final: 0.5578 (t80) REVERT: f 11 LEU cc_start: 0.3453 (mp) cc_final: 0.2909 (mt) REVERT: b 9 LEU cc_start: 0.7389 (mt) cc_final: 0.7013 (mt) REVERT: g 36 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7279 (mmtp) REVERT: g 44 MET cc_start: 0.6679 (mmp) cc_final: 0.5582 (mmm) REVERT: g 108 PHE cc_start: 0.7080 (t80) cc_final: 0.6776 (t80) REVERT: g 148 VAL cc_start: 0.5252 (t) cc_final: 0.4701 (t) REVERT: g 152 LEU cc_start: 0.6833 (mm) cc_final: 0.6315 (tp) REVERT: h 72 VAL cc_start: 0.7464 (t) cc_final: 0.7098 (p) REVERT: h 139 GLU cc_start: 0.5587 (tp30) cc_final: 0.5128 (mm-30) REVERT: h 146 LEU cc_start: 0.5274 (mm) cc_final: 0.5016 (mm) REVERT: i 47 MET cc_start: 0.7608 (mpp) cc_final: 0.7312 (mpp) REVERT: j 52 ILE cc_start: 0.4799 (mp) cc_final: 0.4407 (mp) REVERT: j 53 MET cc_start: 0.3718 (mmt) cc_final: 0.3493 (mmt) REVERT: k 28 MET cc_start: 0.5369 (mmt) cc_final: 0.4101 (ptm) REVERT: k 44 MET cc_start: 0.6005 (tmm) cc_final: 0.5597 (tmm) REVERT: k 76 ILE cc_start: 0.7847 (mt) cc_final: 0.7602 (mt) REVERT: k 104 LEU cc_start: 0.7161 (tp) cc_final: 0.6869 (tp) REVERT: l 25 PHE cc_start: 0.6862 (m-10) cc_final: 0.6048 (m-80) REVERT: m 84 ILE cc_start: 0.7188 (tp) cc_final: 0.6891 (tt) REVERT: m 86 LEU cc_start: 0.1474 (tp) cc_final: 0.0889 (tp) REVERT: n 54 LYS cc_start: 0.4709 (tppt) cc_final: 0.4307 (tppt) REVERT: n 85 THR cc_start: 0.2293 (p) cc_final: 0.1481 (m) REVERT: n 112 ILE cc_start: 0.6842 (tt) cc_final: 0.6565 (mm) REVERT: o 28 MET cc_start: 0.6104 (ptt) cc_final: 0.5855 (ptt) REVERT: o 76 ILE cc_start: 0.6818 (mt) cc_final: 0.6506 (mt) REVERT: X 82 GLN cc_start: 0.5169 (tm-30) cc_final: 0.4599 (mm-40) REVERT: d 240 LEU cc_start: 0.6189 (mt) cc_final: 0.5882 (mt) REVERT: d 323 GLU cc_start: 0.7766 (pp20) cc_final: 0.5907 (mm-30) REVERT: p 331 MET cc_start: 0.3385 (mmm) cc_final: -0.1393 (ttt) REVERT: 1 22 HIS cc_start: 0.7658 (t-90) cc_final: 0.7434 (t-90) REVERT: 1 56 ARG cc_start: 0.7390 (ttm170) cc_final: 0.7141 (ttm170) REVERT: 1 203 PHE cc_start: 0.7112 (m-80) cc_final: 0.6610 (m-10) REVERT: 1 205 MET cc_start: 0.7537 (ptp) cc_final: 0.7271 (ptp) REVERT: 1 228 LEU cc_start: 0.8286 (tp) cc_final: 0.8040 (tt) REVERT: 1 324 GLU cc_start: 0.8188 (tt0) cc_final: 0.7825 (tt0) REVERT: 1 340 MET cc_start: 0.7240 (ttp) cc_final: 0.6482 (ttt) REVERT: 1 550 MET cc_start: 0.7608 (tpt) cc_final: 0.6547 (mtt) REVERT: 1 567 TRP cc_start: 0.6650 (t60) cc_final: 0.5382 (t60) REVERT: 1 571 ARG cc_start: 0.6622 (mtm110) cc_final: 0.6213 (mtm110) REVERT: 1 592 ASP cc_start: 0.7320 (m-30) cc_final: 0.7017 (m-30) REVERT: 1 596 LYS cc_start: 0.7997 (tttt) cc_final: 0.7512 (tptp) REVERT: 0 20 TYR cc_start: 0.7027 (p90) cc_final: 0.6679 (p90) REVERT: 0 293 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7384 (mt-10) REVERT: 0 306 MET cc_start: 0.8291 (tpt) cc_final: 0.7713 (tpp) REVERT: 0 360 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8302 (tm-30) REVERT: 2 104 ARG cc_start: 0.7501 (tpp-160) cc_final: 0.7201 (mtt90) REVERT: 2 364 ARG cc_start: 0.7246 (tpm170) cc_final: 0.5663 (ptm160) REVERT: 2 381 ARG cc_start: 0.8399 (mmp80) cc_final: 0.7911 (mmt180) REVERT: 2 456 LYS cc_start: 0.8414 (ttpt) cc_final: 0.7887 (tptt) REVERT: 2 530 ARG cc_start: 0.5727 (mtt180) cc_final: 0.4070 (mtm110) REVERT: 2 584 MET cc_start: 0.6808 (mmm) cc_final: 0.6230 (mmm) REVERT: 3 106 ASP cc_start: 0.8454 (t0) cc_final: 0.8227 (t70) REVERT: 3 112 CYS cc_start: 0.8163 (t) cc_final: 0.7955 (t) REVERT: 3 174 ILE cc_start: 0.6409 (mm) cc_final: 0.6058 (mm) REVERT: 3 187 GLN cc_start: 0.8517 (mm-40) cc_final: 0.7648 (mm-40) REVERT: 3 326 TYR cc_start: 0.8204 (p90) cc_final: 0.6727 (p90) REVERT: 3 368 LEU cc_start: 0.8929 (mt) cc_final: 0.8580 (mt) REVERT: 3 402 MET cc_start: 0.7467 (tpp) cc_final: 0.7151 (tpp) REVERT: 3 497 GLN cc_start: 0.7470 (mt0) cc_final: 0.6700 (mm110) REVERT: 4 40 LEU cc_start: 0.8806 (tp) cc_final: 0.8249 (mm) REVERT: 4 54 ASN cc_start: 0.8433 (t0) cc_final: 0.7962 (t0) REVERT: 4 70 GLU cc_start: 0.7698 (pt0) cc_final: 0.7124 (pt0) REVERT: 4 170 ILE cc_start: 0.8242 (mt) cc_final: 0.7929 (tt) REVERT: 4 308 ARG cc_start: 0.8204 (ttp-170) cc_final: 0.7764 (ttm170) REVERT: 4 435 MET cc_start: 0.6881 (ppp) cc_final: 0.6332 (ppp) REVERT: 4 455 LEU cc_start: 0.7158 (mt) cc_final: 0.6719 (tt) REVERT: 4 493 LYS cc_start: 0.6517 (mppt) cc_final: 0.5529 (mmtt) REVERT: 5 100 GLU cc_start: 0.8641 (mp0) cc_final: 0.8134 (tp30) REVERT: 5 112 CYS cc_start: 0.8531 (t) cc_final: 0.8124 (t) REVERT: 5 127 MET cc_start: 0.8506 (mmt) cc_final: 0.7778 (mmt) REVERT: 5 244 PHE cc_start: 0.8783 (m-80) cc_final: 0.8225 (m-80) REVERT: 5 299 ASP cc_start: 0.6801 (t0) cc_final: 0.6460 (t0) REVERT: 5 309 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8386 (tm-30) REVERT: 5 321 ARG cc_start: 0.7222 (tpp80) cc_final: 0.6555 (tpp80) outliers start: 3 outliers final: 0 residues processed: 1492 average time/residue: 0.6025 time to fit residues: 1537.1220 Evaluate side-chains 1296 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1296 time to evaluate : 5.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 523 optimal weight: 0.0670 chunk 701 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 607 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 659 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 677 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 10 GLN ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 GLN 6 131 GLN 6 336 HIS ** U 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 85 ASN ** a 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 397 ASN ** a 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 148 ASN ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN j 124 GLN d 108 ASN ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 387 GLN ** 0 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 468 HIS 2 65 GLN ** 2 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 HIS ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.209736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.180830 restraints weight = 139567.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.174205 restraints weight = 143351.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.170855 restraints weight = 115174.619| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 66773 Z= 0.186 Angle : 0.609 12.169 90244 Z= 0.317 Chirality : 0.042 0.304 10230 Planarity : 0.004 0.068 11573 Dihedral : 4.555 69.672 9103 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 0.07 % Allowed : 0.31 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.09), residues: 8314 helix: 1.51 (0.08), residues: 4659 sheet: -0.72 (0.22), residues: 624 loop : -1.34 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.001 TRP 6 282 HIS 0.009 0.001 HIS U 370 PHE 0.032 0.002 PHE b 96 TYR 0.048 0.001 TYR m 68 ARG 0.011 0.000 ARG 7 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21564.75 seconds wall clock time: 373 minutes 36.11 seconds (22416.11 seconds total)