Starting phenix.real_space_refine on Thu Mar 21 13:26:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbu_21144/03_2024/6vbu_21144.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbu_21144/03_2024/6vbu_21144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbu_21144/03_2024/6vbu_21144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbu_21144/03_2024/6vbu_21144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbu_21144/03_2024/6vbu_21144.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbu_21144/03_2024/6vbu_21144.pdb" } resolution = 3.1 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 149 5.16 5 C 19254 2.51 5 N 5162 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 25": "OD1" <-> "OD2" Residue "1 PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 29": "OD1" <-> "OD2" Residue "1 GLU 31": "OE1" <-> "OE2" Residue "1 ARG 44": "NH1" <-> "NH2" Residue "1 ASP 214": "OD1" <-> "OD2" Residue "1 PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 277": "NH1" <-> "NH2" Residue "1 TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 341": "NH1" <-> "NH2" Residue "1 GLU 354": "OE1" <-> "OE2" Residue "1 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 380": "NH1" <-> "NH2" Residue "1 ARG 429": "NH1" <-> "NH2" Residue "1 ASP 436": "OD1" <-> "OD2" Residue "1 ARG 440": "NH1" <-> "NH2" Residue "1 TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 465": "NH1" <-> "NH2" Residue "1 ARG 483": "NH1" <-> "NH2" Residue "1 GLU 484": "OE1" <-> "OE2" Residue "1 PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 512": "NH1" <-> "NH2" Residue "1 PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 532": "NH1" <-> "NH2" Residue "1 PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 588": "OE1" <-> "OE2" Residue "2 ARG 23": "NH1" <-> "NH2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 104": "OD1" <-> "OD2" Residue "2 PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 114": "NH1" <-> "NH2" Residue "2 ASP 153": "OD1" <-> "OD2" Residue "2 ASP 161": "OD1" <-> "OD2" Residue "2 GLU 193": "OE1" <-> "OE2" Residue "2 GLU 195": "OE1" <-> "OE2" Residue "2 TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 251": "OD1" <-> "OD2" Residue "2 ASP 270": "OD1" <-> "OD2" Residue "2 ARG 275": "NH1" <-> "NH2" Residue "2 GLU 278": "OE1" <-> "OE2" Residue "2 PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 296": "OD1" <-> "OD2" Residue "2 ARG 298": "NH1" <-> "NH2" Residue "2 ASP 311": "OD1" <-> "OD2" Residue "2 ARG 315": "NH1" <-> "NH2" Residue "2 TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 356": "OE1" <-> "OE2" Residue "2 ARG 413": "NH1" <-> "NH2" Residue "2 PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 426": "OE1" <-> "OE2" Residue "2 PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 476": "NH1" <-> "NH2" Residue "2 ARG 509": "NH1" <-> "NH2" Residue "2 GLU 522": "OE1" <-> "OE2" Residue "2 PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 562": "OD1" <-> "OD2" Residue "2 PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 578": "OE1" <-> "OE2" Residue "2 GLU 591": "OE1" <-> "OE2" Residue "2 GLU 602": "OE1" <-> "OE2" Residue "2 ASP 613": "OD1" <-> "OD2" Residue "2 ARG 632": "NH1" <-> "NH2" Residue "2 ARG 635": "NH1" <-> "NH2" Residue "2 TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 661": "NH1" <-> "NH2" Residue "2 ARG 686": "NH1" <-> "NH2" Residue "2 ARG 699": "NH1" <-> "NH2" Residue "4 GLU 49": "OE1" <-> "OE2" Residue "4 GLU 85": "OE1" <-> "OE2" Residue "4 PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 109": "NH1" <-> "NH2" Residue "4 ASP 152": "OD1" <-> "OD2" Residue "4 TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 362": "OE1" <-> "OE2" Residue "4 TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 389": "NH1" <-> "NH2" Residue "4 TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 399": "OE1" <-> "OE2" Residue "4 GLU 412": "OE1" <-> "OE2" Residue "5 ARG 11": "NH1" <-> "NH2" Residue "5 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 25": "NH1" <-> "NH2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "5 ARG 66": "NH1" <-> "NH2" Residue "5 ARG 82": "NH1" <-> "NH2" Residue "5 ARG 89": "NH1" <-> "NH2" Residue "5 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 107": "OE1" <-> "OE2" Residue "5 ARG 119": "NH1" <-> "NH2" Residue "5 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 138": "NH1" <-> "NH2" Residue "5 ARG 143": "NH1" <-> "NH2" Residue "5 ASP 173": "OD1" <-> "OD2" Residue "5 PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 186": "NH1" <-> "NH2" Residue "5 ARG 207": "NH1" <-> "NH2" Residue "5 GLU 223": "OE1" <-> "OE2" Residue "5 TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 249": "OE1" <-> "OE2" Residue "5 TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 53": "OE1" <-> "OE2" Residue "7 PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 68": "NH1" <-> "NH2" Residue "7 GLU 70": "OE1" <-> "OE2" Residue "7 PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 134": "OD1" <-> "OD2" Residue "7 ASP 145": "OD1" <-> "OD2" Residue "7 ASP 149": "OD1" <-> "OD2" Residue "7 GLU 156": "OE1" <-> "OE2" Residue "7 ARG 160": "NH1" <-> "NH2" Residue "7 ASP 179": "OD1" <-> "OD2" Residue "7 GLU 185": "OE1" <-> "OE2" Residue "7 GLU 235": "OE1" <-> "OE2" Residue "7 ASP 252": "OD1" <-> "OD2" Residue "7 ASP 262": "OD1" <-> "OD2" Residue "7 TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 276": "OE1" <-> "OE2" Residue "7 ASP 282": "OD1" <-> "OD2" Residue "7 ASP 303": "OD1" <-> "OD2" Residue "7 TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 337": "OE1" <-> "OE2" Residue "7 ARG 346": "NH1" <-> "NH2" Residue "7 GLU 348": "OE1" <-> "OE2" Residue "7 GLU 361": "OE1" <-> "OE2" Residue "7 PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 391": "OD1" <-> "OD2" Residue "7 TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 405": "OD1" <-> "OD2" Residue "7 ASP 416": "OD1" <-> "OD2" Residue "7 ASP 419": "OD1" <-> "OD2" Residue "7 PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 446": "NH1" <-> "NH2" Residue "7 GLU 455": "OE1" <-> "OE2" Residue "7 TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 475": "NH1" <-> "NH2" Residue "7 TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 551": "OD1" <-> "OD2" Residue "7 ASP 568": "OD1" <-> "OD2" Residue "7 ASP 578": "OD1" <-> "OD2" Residue "7 TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 614": "OE1" <-> "OE2" Residue "7 GLU 631": "OE1" <-> "OE2" Residue "7 GLU 651": "OE1" <-> "OE2" Residue "7 GLU 652": "OE1" <-> "OE2" Residue "7 GLU 658": "OE1" <-> "OE2" Residue "7 ASP 680": "OD1" <-> "OD2" Residue "7 PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 698": "OE1" <-> "OE2" Residue "7 PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 12": "NH1" <-> "NH2" Residue "8 ARG 14": "NH1" <-> "NH2" Residue "8 GLU 28": "OE1" <-> "OE2" Residue "8 ARG 42": "NH1" <-> "NH2" Residue "8 GLU 57": "OE1" <-> "OE2" Residue "8 GLU 62": "OE1" <-> "OE2" Residue "8 ASP 66": "OD1" <-> "OD2" Residue "8 ARG 110": "NH1" <-> "NH2" Residue "8 GLU 122": "OE1" <-> "OE2" Residue "8 ARG 129": "NH1" <-> "NH2" Residue "8 PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 223": "NH1" <-> "NH2" Residue "8 ARG 228": "NH1" <-> "NH2" Residue "8 PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 272": "OD1" <-> "OD2" Residue "8 GLU 277": "OE1" <-> "OE2" Residue "8 GLU 289": "OE1" <-> "OE2" Residue "8 GLU 290": "OE1" <-> "OE2" Residue "8 TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 326": "OD1" <-> "OD2" Residue "8 ARG 333": "NH1" <-> "NH2" Residue "8 PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 337": "NH1" <-> "NH2" Residue "8 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 370": "OE1" <-> "OE2" Residue "8 ARG 371": "NH1" <-> "NH2" Residue "8 TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 418": "OE1" <-> "OE2" Residue "8 ARG 429": "NH1" <-> "NH2" Residue "8 PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 483": "OD1" <-> "OD2" Residue "9 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 7": "NH1" <-> "NH2" Residue "9 ASP 31": "OD1" <-> "OD2" Residue "9 ARG 50": "NH1" <-> "NH2" Residue "9 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 71": "OE1" <-> "OE2" Residue "9 ARG 75": "NH1" <-> "NH2" Residue "9 GLU 116": "OE1" <-> "OE2" Residue "9 TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 149": "NH1" <-> "NH2" Residue "9 ARG 173": "NH1" <-> "NH2" Residue "9 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 189": "NH1" <-> "NH2" Residue "9 GLU 203": "OE1" <-> "OE2" Residue "9 TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 247": "OD1" <-> "OD2" Residue "9 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 340": "OD1" <-> "OD2" Residue "9 ASP 362": "OD1" <-> "OD2" Residue "9 PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 499": "OE1" <-> "OE2" Residue "9 TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 513": "OE1" <-> "OE2" Residue "9 ARG 514": "NH1" <-> "NH2" Residue "9 ASP 517": "OD1" <-> "OD2" Residue "9 ARG 528": "NH1" <-> "NH2" Residue "9 PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 600": "NH1" <-> "NH2" Residue "9 PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 608": "OD1" <-> "OD2" Residue "9 TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 631": "OD1" <-> "OD2" Residue "9 GLU 643": "OE1" <-> "OE2" Residue "9 TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 656": "NH1" <-> "NH2" Residue "9 GLU 664": "OE1" <-> "OE2" Residue "9 ARG 669": "NH1" <-> "NH2" Residue "9 PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 679": "NH1" <-> "NH2" Residue "9 TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 765": "OE1" <-> "OE2" Residue "9 PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30209 Number of models: 1 Model: "" Number of chains: 9 Chain: "0" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 421 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "1" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3767 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 29, 'TRANS': 456} Chain breaks: 3 Chain: "2" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5145 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 22, 'TRANS': 636} Chain breaks: 4 Chain: "4" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3113 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain breaks: 1 Chain: "5" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2411 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "7" Number of atoms: 5519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5519 Classifications: {'peptide': 698} Link IDs: {'PTRANS': 25, 'TRANS': 672} Chain breaks: 2 Chain: "8" Number of atoms: 3797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3797 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 20, 'TRANS': 454} Chain breaks: 2 Chain: "9" Number of atoms: 6034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6034 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 31, 'TRANS': 732} Chain breaks: 5 Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.97, per 1000 atoms: 0.50 Number of scatterers: 30209 At special positions: 0 Unit cell: (152.64, 184.44, 172.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 149 16.00 O 5642 8.00 N 5162 7.00 C 19254 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: 10.55 Conformation dependent library (CDL) restraints added in 5.2 seconds 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7198 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 48 sheets defined 35.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain '0' and resid 38 through 57 Processing helix chain '1' and resid 431 through 444 removed outlier: 3.740A pdb=" N VAL 1 435 " --> pdb=" O THR 1 431 " (cutoff:3.500A) Processing helix chain '1' and resid 444 through 474 removed outlier: 3.714A pdb=" N MET 1 448 " --> pdb=" O ALA 1 444 " (cutoff:3.500A) Processing helix chain '2' and resid 339 through 358 removed outlier: 3.685A pdb=" N ASN 2 358 " --> pdb=" O ASN 2 354 " (cutoff:3.500A) Processing helix chain '2' and resid 490 through 494 removed outlier: 3.970A pdb=" N GLU 2 494 " --> pdb=" O PRO 2 491 " (cutoff:3.500A) Processing helix chain '2' and resid 506 through 517 Processing helix chain '2' and resid 560 through 575 Processing helix chain '2' and resid 586 through 634 removed outlier: 3.547A pdb=" N GLU 2 592 " --> pdb=" O VAL 2 588 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP 2 601 " --> pdb=" O LEU 2 597 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU 2 602 " --> pdb=" O VAL 2 598 " (cutoff:3.500A) Processing helix chain '2' and resid 636 through 685 Processing helix chain '2' and resid 689 through 704 removed outlier: 3.525A pdb=" N GLN 2 693 " --> pdb=" O LYS 2 689 " (cutoff:3.500A) Processing helix chain '2' and resid 706 through 716 Processing helix chain '4' and resid 36 through 45 Processing helix chain '4' and resid 49 through 63 removed outlier: 3.745A pdb=" N ALA 4 53 " --> pdb=" O GLU 4 49 " (cutoff:3.500A) Processing helix chain '4' and resid 68 through 80 removed outlier: 3.519A pdb=" N VAL 4 72 " --> pdb=" O TYR 4 68 " (cutoff:3.500A) Processing helix chain '4' and resid 82 through 97 removed outlier: 3.628A pdb=" N SER 4 86 " --> pdb=" O ASN 4 82 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG 4 88 " --> pdb=" O GLN 4 84 " (cutoff:3.500A) Processing helix chain '4' and resid 100 through 113 removed outlier: 3.870A pdb=" N LEU 4 104 " --> pdb=" O CYS 4 100 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 131 removed outlier: 3.844A pdb=" N GLU 4 126 " --> pdb=" O GLU 4 122 " (cutoff:3.500A) Processing helix chain '4' and resid 134 through 148 removed outlier: 4.097A pdb=" N CYS 4 138 " --> pdb=" O ASP 4 134 " (cutoff:3.500A) Processing helix chain '4' and resid 150 through 165 Processing helix chain '4' and resid 167 through 182 removed outlier: 3.568A pdb=" N TYR 4 171 " --> pdb=" O HIS 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 197 removed outlier: 4.174A pdb=" N ALA 4 187 " --> pdb=" O ASP 4 183 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLU 4 189 " --> pdb=" O ASP 4 185 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE 4 197 " --> pdb=" O LYS 4 193 " (cutoff:3.500A) Processing helix chain '4' and resid 201 through 215 removed outlier: 3.506A pdb=" N LEU 4 205 " --> pdb=" O ASN 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 218 through 232 Processing helix chain '4' and resid 235 through 249 Processing helix chain '4' and resid 251 through 263 removed outlier: 3.804A pdb=" N VAL 4 262 " --> pdb=" O LYS 4 258 " (cutoff:3.500A) Processing helix chain '4' and resid 269 through 283 Processing helix chain '4' and resid 285 through 299 removed outlier: 3.559A pdb=" N LEU 4 299 " --> pdb=" O ARG 4 295 " (cutoff:3.500A) Processing helix chain '4' and resid 303 through 317 removed outlier: 3.805A pdb=" N LEU 4 307 " --> pdb=" O ASP 4 303 " (cutoff:3.500A) Processing helix chain '4' and resid 322 through 334 Processing helix chain '4' and resid 337 through 350 removed outlier: 3.927A pdb=" N TYR 4 341 " --> pdb=" O MET 4 337 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN 4 350 " --> pdb=" O VAL 4 346 " (cutoff:3.500A) Processing helix chain '4' and resid 354 through 368 Processing helix chain '4' and resid 372 through 385 Processing helix chain '4' and resid 390 through 400 Processing helix chain '4' and resid 412 through 423 removed outlier: 3.809A pdb=" N GLU 4 416 " --> pdb=" O GLU 4 412 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET 4 417 " --> pdb=" O PHE 4 413 " (cutoff:3.500A) Processing helix chain '5' and resid 119 through 134 removed outlier: 3.522A pdb=" N SER 5 123 " --> pdb=" O ARG 5 119 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE 5 125 " --> pdb=" O TYR 5 121 " (cutoff:3.500A) Processing helix chain '5' and resid 226 through 229 removed outlier: 3.723A pdb=" N GLY 5 229 " --> pdb=" O GLN 5 226 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 226 through 229' Processing helix chain '5' and resid 239 through 260 removed outlier: 4.107A pdb=" N ASN 5 260 " --> pdb=" O VAL 5 256 " (cutoff:3.500A) Processing helix chain '5' and resid 298 through 303 removed outlier: 3.693A pdb=" N PHE 5 303 " --> pdb=" O VAL 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 332 through 338 removed outlier: 3.820A pdb=" N GLU 5 338 " --> pdb=" O GLN 5 334 " (cutoff:3.500A) Processing helix chain '7' and resid 337 through 366 Processing helix chain '7' and resid 367 through 369 No H-bonds generated for 'chain '7' and resid 367 through 369' Processing helix chain '7' and resid 516 through 528 Processing helix chain '7' and resid 570 through 588 Processing helix chain '7' and resid 598 through 637 removed outlier: 4.506A pdb=" N VAL 7 602 " --> pdb=" O ASN 7 598 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS 7 603 " --> pdb=" O GLU 7 599 " (cutoff:3.500A) Proline residue: 7 611 - end of helix removed outlier: 3.983A pdb=" N LEU 7 625 " --> pdb=" O LYS 7 621 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP 7 627 " --> pdb=" O VAL 7 623 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ALA 7 628 " --> pdb=" O GLN 7 624 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS 7 635 " --> pdb=" O GLU 7 631 " (cutoff:3.500A) Processing helix chain '7' and resid 643 through 661 removed outlier: 3.682A pdb=" N ARG 7 647 " --> pdb=" O ILE 7 643 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE 7 649 " --> pdb=" O GLU 7 645 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP 7 654 " --> pdb=" O LEU 7 650 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N HIS 7 655 " --> pdb=" O GLU 7 651 " (cutoff:3.500A) Processing helix chain '7' and resid 662 through 686 Processing helix chain '7' and resid 693 through 695 No H-bonds generated for 'chain '7' and resid 693 through 695' Processing helix chain '7' and resid 696 through 703 Processing helix chain '7' and resid 704 through 715 Processing helix chain '8' and resid 2 through 13 Processing helix chain '8' and resid 17 through 30 Processing helix chain '8' and resid 33 through 48 removed outlier: 3.652A pdb=" N TRP 8 37 " --> pdb=" O ASP 8 33 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL 8 48 " --> pdb=" O LEU 8 44 " (cutoff:3.500A) Processing helix chain '8' and resid 59 through 65 Processing helix chain '8' and resid 121 through 126 Processing helix chain '8' and resid 167 through 172 removed outlier: 3.510A pdb=" N TYR 8 171 " --> pdb=" O ASN 8 167 " (cutoff:3.500A) Processing helix chain '8' and resid 174 through 188 removed outlier: 4.163A pdb=" N ALA 8 180 " --> pdb=" O LYS 8 176 " (cutoff:3.500A) Processing helix chain '8' and resid 191 through 206 Processing helix chain '8' and resid 210 through 225 removed outlier: 3.763A pdb=" N LYS 8 214 " --> pdb=" O ASP 8 210 " (cutoff:3.500A) Processing helix chain '8' and resid 226 through 239 removed outlier: 3.790A pdb=" N GLN 8 233 " --> pdb=" O GLU 8 229 " (cutoff:3.500A) Processing helix chain '8' and resid 243 through 257 Processing helix chain '8' and resid 259 through 274 Processing helix chain '8' and resid 277 through 291 Processing helix chain '8' and resid 293 through 308 removed outlier: 3.750A pdb=" N GLU 8 299 " --> pdb=" O SER 8 295 " (cutoff:3.500A) Processing helix chain '8' and resid 311 through 325 Processing helix chain '8' and resid 327 through 341 Processing helix chain '8' and resid 346 through 360 Processing helix chain '8' and resid 364 through 376 removed outlier: 3.805A pdb=" N SER 8 368 " --> pdb=" O MET 8 364 " (cutoff:3.500A) Processing helix chain '8' and resid 379 through 397 Processing helix chain '8' and resid 398 through 413 Processing helix chain '8' and resid 416 through 431 Processing helix chain '8' and resid 432 through 447 Processing helix chain '8' and resid 450 through 463 removed outlier: 4.167A pdb=" N HIS 8 454 " --> pdb=" O MET 8 450 " (cutoff:3.500A) Processing helix chain '8' and resid 466 through 481 removed outlier: 3.668A pdb=" N LYS 8 476 " --> pdb=" O ALA 8 472 " (cutoff:3.500A) Processing helix chain '8' and resid 484 through 499 Processing helix chain '9' and resid 207 through 213 Processing helix chain '9' and resid 377 through 397 removed outlier: 4.042A pdb=" N ASN 9 396 " --> pdb=" O ILE 9 392 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS 9 397 " --> pdb=" O LYS 9 393 " (cutoff:3.500A) Processing helix chain '9' and resid 530 through 533 Processing helix chain '9' and resid 558 through 563 removed outlier: 3.806A pdb=" N LEU 9 562 " --> pdb=" O SER 9 558 " (cutoff:3.500A) Processing helix chain '9' and resid 608 through 628 removed outlier: 4.234A pdb=" N ILE 9 612 " --> pdb=" O ASP 9 608 " (cutoff:3.500A) Processing helix chain '9' and resid 644 through 686 removed outlier: 4.230A pdb=" N LEU 9 648 " --> pdb=" O GLU 9 644 " (cutoff:3.500A) Processing helix chain '9' and resid 692 through 742 removed outlier: 3.757A pdb=" N GLY 9 701 " --> pdb=" O THR 9 697 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER 9 729 " --> pdb=" O THR 9 725 " (cutoff:3.500A) Processing helix chain '9' and resid 745 through 757 removed outlier: 3.579A pdb=" N LEU 9 752 " --> pdb=" O GLN 9 748 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU 9 757 " --> pdb=" O GLU 9 753 " (cutoff:3.500A) Processing helix chain '9' and resid 767 through 784 removed outlier: 3.868A pdb=" N THR 9 771 " --> pdb=" O GLY 9 767 " (cutoff:3.500A) Processing helix chain '9' and resid 787 through 794 Processing helix chain '9' and resid 805 through 821 Processing sheet with id=AA1, first strand: chain '0' and resid 36 through 37 removed outlier: 6.206A pdb=" N LEU 0 36 " --> pdb=" O LEU 8 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '1' and resid 3 through 9 removed outlier: 5.407A pdb=" N ASP 1 5 " --> pdb=" O ILE 1 401 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE 1 401 " --> pdb=" O ASP 1 5 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLY 1 396 " --> pdb=" O THR 1 392 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR 1 392 " --> pdb=" O GLY 1 396 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN 1 386 " --> pdb=" O LEU 1 402 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ASP 1 385 " --> pdb=" O TYR 1 381 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR 1 381 " --> pdb=" O ASP 1 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 21 through 24 removed outlier: 4.000A pdb=" N ASP 1 38 " --> pdb=" O ARG 1 47 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER 1 58 " --> pdb=" O VAL 1 50 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS 1 52 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU 1 56 " --> pdb=" O LYS 1 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 68 through 71 removed outlier: 4.335A pdb=" N ALA 1 68 " --> pdb=" O ALA 1 87 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS 1 96 " --> pdb=" O PRO 1 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 200 through 207 removed outlier: 3.819A pdb=" N THR 1 202 " --> pdb=" O GLY 1 222 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU 1 227 " --> pdb=" O THR 1 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 248 through 256 removed outlier: 4.343A pdb=" N SER 1 271 " --> pdb=" O CYS 1 267 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 292 through 297 removed outlier: 3.957A pdb=" N GLY 1 294 " --> pdb=" O GLY 1 305 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER 1 310 " --> pdb=" O SER 1 306 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR 1 315 " --> pdb=" O ARG 1 320 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG 1 320 " --> pdb=" O THR 1 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 330 through 335 removed outlier: 3.961A pdb=" N ALA 1 332 " --> pdb=" O ALA 1 349 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET 1 347 " --> pdb=" O ASN 1 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '1' and resid 354 through 355 Processing sheet with id=AB1, first strand: chain '1' and resid 486 through 493 Processing sheet with id=AB2, first strand: chain '1' and resid 535 through 536 Processing sheet with id=AB3, first strand: chain '2' and resid 6 through 9 removed outlier: 4.369A pdb=" N GLU 2 313 " --> pdb=" O SER 2 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '2' and resid 14 through 23 removed outlier: 6.973A pdb=" N MET 2 18 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '2' and resid 75 through 81 Processing sheet with id=AB6, first strand: chain '2' and resid 122 through 123 Processing sheet with id=AB7, first strand: chain '2' and resid 144 through 147 removed outlier: 6.776A pdb=" N LEU 2 144 " --> pdb=" O TRP 2 156 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP 2 156 " --> pdb=" O LEU 2 144 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY 2 146 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 163 through 167 removed outlier: 3.819A pdb=" N SER 2 165 " --> pdb=" O GLY 2 182 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP 2 187 " --> pdb=" O SER 2 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 208 through 213 removed outlier: 6.958A pdb=" N ARG 2 216 " --> pdb=" O MET 2 212 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL 2 226 " --> pdb=" O ARG 2 237 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG 2 237 " --> pdb=" O VAL 2 226 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL 2 228 " --> pdb=" O TYR 2 235 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '2' and resid 246 through 250 removed outlier: 3.599A pdb=" N SER 2 246 " --> pdb=" O GLY 2 263 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG 2 272 " --> pdb=" O LEU 2 260 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL 2 269 " --> pdb=" O LYS 2 282 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS 2 282 " --> pdb=" O VAL 2 269 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA 2 271 " --> pdb=" O ILE 2 280 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '2' and resid 377 through 378 Processing sheet with id=AC3, first strand: chain '2' and resid 383 through 390 Processing sheet with id=AC4, first strand: chain '2' and resid 427 through 430 removed outlier: 4.861A pdb=" N ILE 2 412 " --> pdb=" O GLY 2 462 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY 2 462 " --> pdb=" O ILE 2 412 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA 2 414 " --> pdb=" O PHE 2 460 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR 7 480 " --> pdb=" O PRO 7 474 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN 7 406 " --> pdb=" O THR 7 473 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU 7 441 " --> pdb=" O SER 7 411 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '2' and resid 485 through 486 Processing sheet with id=AC6, first strand: chain '5' and resid 13 through 15 removed outlier: 3.970A pdb=" N ARG 5 56 " --> pdb=" O THR 5 53 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLY 5 48 " --> pdb=" O SER 5 36 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA 5 94 " --> pdb=" O THR 5 81 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR 5 81 " --> pdb=" O ALA 5 94 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR 5 96 " --> pdb=" O ILE 5 79 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE 5 79 " --> pdb=" O TYR 5 96 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU 5 98 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 141 through 142 removed outlier: 4.190A pdb=" N ARG 5 186 " --> pdb=" O THR 5 183 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLY 5 178 " --> pdb=" O GLY 5 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 206 through 210 Processing sheet with id=AC9, first strand: chain '5' and resid 314 through 316 Processing sheet with id=AD1, first strand: chain '7' and resid 6 through 12 removed outlier: 4.811A pdb=" N ILE 7 314 " --> pdb=" O TYR 7 10 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '7' and resid 21 through 24 removed outlier: 6.786A pdb=" N CYS 7 46 " --> pdb=" O VAL 7 57 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '7' and resid 69 through 72 removed outlier: 6.359A pdb=" N ILE 7 90 " --> pdb=" O SER 7 102 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER 7 102 " --> pdb=" O ILE 7 90 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY 7 92 " --> pdb=" O PHE 7 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '7' and resid 114 through 117 removed outlier: 6.407A pdb=" N CYS 7 133 " --> pdb=" O ASP 7 137 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP 7 137 " --> pdb=" O CYS 7 133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '7' and resid 147 through 152 removed outlier: 7.016A pdb=" N ALA 7 166 " --> pdb=" O ASN 7 148 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL 7 150 " --> pdb=" O VAL 7 164 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL 7 164 " --> pdb=" O VAL 7 150 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '7' and resid 171 through 176 removed outlier: 6.393A pdb=" N LEU 7 172 " --> pdb=" O GLU 7 183 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU 7 183 " --> pdb=" O LEU 7 172 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL 7 174 " --> pdb=" O THR 7 181 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '7' and resid 190 through 193 removed outlier: 4.751A pdb=" N LYS 7 215 " --> pdb=" O THR 7 211 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU 7 216 " --> pdb=" O GLU 7 231 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU 7 231 " --> pdb=" O LEU 7 216 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU 7 218 " --> pdb=" O LYS 7 229 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS 7 229 " --> pdb=" O LEU 7 218 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '7' and resid 243 through 246 removed outlier: 3.755A pdb=" N CYS 7 243 " --> pdb=" O GLY 7 260 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE 7 281 " --> pdb=" O VAL 7 268 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY 7 270 " --> pdb=" O LEU 7 279 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU 7 279 " --> pdb=" O GLY 7 270 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '7' and resid 384 through 387 removed outlier: 3.687A pdb=" N THR 7 386 " --> pdb=" O SER 7 395 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '7' and resid 494 through 497 removed outlier: 4.378A pdb=" N TYR 7 544 " --> pdb=" O THR 7 497 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE 7 545 " --> pdb=" O LEU 7 554 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU 7 562 " --> pdb=" O ARG 7 559 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '9' and resid 6 through 13 removed outlier: 5.209A pdb=" N ASP 9 8 " --> pdb=" O TYR 9 358 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TYR 9 358 " --> pdb=" O ASP 9 8 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRP 9 10 " --> pdb=" O CYS 9 356 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '9' and resid 25 through 28 removed outlier: 3.574A pdb=" N ALA 9 28 " --> pdb=" O LYS 9 39 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '9' and resid 80 through 84 removed outlier: 3.824A pdb=" N LEU 9 95 " --> pdb=" O TYR 9 106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '9' and resid 108 through 111 Processing sheet with id=AE6, first strand: chain '9' and resid 135 through 141 removed outlier: 3.604A pdb=" N ASN 9 137 " --> pdb=" O GLN 9 155 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET 9 160 " --> pdb=" O SER 9 156 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU 9 161 " --> pdb=" O GLY 9 172 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY 9 172 " --> pdb=" O LEU 9 161 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL 9 163 " --> pdb=" O ALA 9 170 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '9' and resid 184 through 187 removed outlier: 6.732A pdb=" N LYS 9 206 " --> pdb=" O VAL 9 235 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL 9 235 " --> pdb=" O LYS 9 206 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '9' and resid 245 through 251 removed outlier: 3.603A pdb=" N ASP 9 247 " --> pdb=" O LEU 9 263 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL 9 251 " --> pdb=" O SER 9 259 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER 9 259 " --> pdb=" O VAL 9 251 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '9' and resid 287 through 291 removed outlier: 3.751A pdb=" N CYS 9 289 " --> pdb=" O GLY 9 306 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET 9 311 " --> pdb=" O ASN 9 307 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU 9 312 " --> pdb=" O ALA 9 323 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA 9 323 " --> pdb=" O LEU 9 312 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE 9 314 " --> pdb=" O LYS 9 321 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '9' and resid 411 through 417 Processing sheet with id=AF2, first strand: chain '9' and resid 471 through 477 removed outlier: 7.026A pdb=" N GLN 9 471 " --> pdb=" O SER 9 458 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER 9 458 " --> pdb=" O GLN 9 471 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR 9 473 " --> pdb=" O LYS 9 456 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS 9 456 " --> pdb=" O THR 9 473 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU 9 475 " --> pdb=" O LYS 9 454 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 9 452 " --> pdb=" O MET 9 477 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS 9 454 " --> pdb=" O SER 9 509 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER 9 509 " --> pdb=" O LYS 9 454 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '9' and resid 535 through 537 1515 hydrogen bonds defined for protein. 4350 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: 10.90 Time building geometry restraints manager: 11.58 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: 8441 1.33 - 1.45: 5049 1.45 - 1.57: 17077 1.57 - 1.69: 1 1.69 - 1.81: 223 Bond restraints: 30791 Sorted by residual: bond pdb=" N LEU 0 12 " pdb=" CA LEU 0 12 " ideal model delta sigma weight residual 1.453 1.484 -0.030 8.30e-03 1.45e+04 1.34e+01 bond pdb=" C ALA 9 478 " pdb=" N PRO 9 479 " ideal model delta sigma weight residual 1.332 1.375 -0.043 1.26e-02 6.30e+03 1.17e+01 bond pdb=" N VAL 9 202 " pdb=" CA VAL 9 202 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.08e-02 8.57e+03 1.06e+01 bond pdb=" N GLN 0 17 " pdb=" CA GLN 0 17 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.39e+00 bond pdb=" N LEU 0 18 " pdb=" CA LEU 0 18 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.23e-02 6.61e+03 8.15e+00 ... (remaining 30786 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.32: 735 106.32 - 113.32: 17072 113.32 - 120.33: 11378 120.33 - 127.33: 12215 127.33 - 134.34: 271 Bond angle restraints: 41671 Sorted by residual: angle pdb=" N ARG 7 360 " pdb=" CA ARG 7 360 " pdb=" C ARG 7 360 " ideal model delta sigma weight residual 111.14 103.94 7.20 1.08e+00 8.57e-01 4.44e+01 angle pdb=" C ALA 9 478 " pdb=" N PRO 9 479 " pdb=" CA PRO 9 479 " ideal model delta sigma weight residual 119.92 125.34 -5.42 1.07e+00 8.73e-01 2.56e+01 angle pdb=" N LYS 2 192 " pdb=" CA LYS 2 192 " pdb=" C LYS 2 192 " ideal model delta sigma weight residual 110.50 103.95 6.55 1.41e+00 5.03e-01 2.16e+01 angle pdb=" N GLN 5 205 " pdb=" CA GLN 5 205 " pdb=" C GLN 5 205 " ideal model delta sigma weight residual 113.41 108.30 5.11 1.22e+00 6.72e-01 1.75e+01 angle pdb=" C TYR 2 644 " pdb=" CA TYR 2 644 " pdb=" CB TYR 2 644 " ideal model delta sigma weight residual 110.79 117.61 -6.82 1.66e+00 3.63e-01 1.69e+01 ... (remaining 41666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16641 17.96 - 35.91: 1640 35.91 - 53.87: 266 53.87 - 71.82: 38 71.82 - 89.78: 38 Dihedral angle restraints: 18623 sinusoidal: 7490 harmonic: 11133 Sorted by residual: dihedral pdb=" CA THR 5 40 " pdb=" C THR 5 40 " pdb=" N LYS 5 41 " pdb=" CA LYS 5 41 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ASN 9 307 " pdb=" C ASN 9 307 " pdb=" N HIS 9 308 " pdb=" CA HIS 9 308 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA GLU 1 224 " pdb=" C GLU 1 224 " pdb=" N ASN 1 225 " pdb=" CA ASN 1 225 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 18620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4112 0.066 - 0.132: 582 0.132 - 0.198: 43 0.198 - 0.263: 8 0.263 - 0.329: 4 Chirality restraints: 4749 Sorted by residual: chirality pdb=" CA TYR 9 315 " pdb=" N TYR 9 315 " pdb=" C TYR 9 315 " pdb=" CB TYR 9 315 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA TYR 2 644 " pdb=" N TYR 2 644 " pdb=" C TYR 2 644 " pdb=" CB TYR 2 644 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA ASP 2 194 " pdb=" N ASP 2 194 " pdb=" C ASP 2 194 " pdb=" CB ASP 2 194 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4746 not shown) Planarity restraints: 5343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS 2 689 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO 2 690 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO 2 690 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO 2 690 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 5 155 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO 5 156 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO 5 156 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO 5 156 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN 9 462 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO 9 463 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO 9 463 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO 9 463 " 0.026 5.00e-02 4.00e+02 ... (remaining 5340 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 465 2.66 - 3.22: 28293 3.22 - 3.78: 46018 3.78 - 4.34: 65529 4.34 - 4.90: 108829 Nonbonded interactions: 249134 Sorted by model distance: nonbonded pdb=" OE2 GLU 2 178 " pdb="CA CA 2 801 " model vdw 2.096 2.510 nonbonded pdb=" OH TYR 4 71 " pdb=" OD1 ASP 4 102 " model vdw 2.208 2.440 nonbonded pdb=" O LYS 2 176 " pdb="CA CA 2 801 " model vdw 2.217 2.510 nonbonded pdb=" OG SER 9 156 " pdb=" OD1 ASP 9 158 " model vdw 2.224 2.440 nonbonded pdb=" O ASP 2 194 " pdb=" ND2 ASN 2 692 " model vdw 2.229 2.520 ... (remaining 249129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 0.030 Extract box with map and model: 8.610 Check model and map are aligned: 0.460 Set scattering table: 0.240 Process input model: 74.370 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.005 0.043 30791 Z= 0.297 Angle : 0.688 7.652 41671 Z= 0.400 Chirality : 0.047 0.329 4749 Planarity : 0.004 0.062 5343 Dihedral : 14.738 89.780 11425 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.24 % Allowed : 5.70 % Favored : 94.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -3.06 (0.12), residues: 3766 helix: -0.78 (0.13), residues: 1309 sheet: -1.83 (0.16), residues: 923 loop : -3.25 (0.13), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 1 322 HIS 0.008 0.001 HIS 7 131 PHE 0.022 0.002 PHE 9 290 TYR 0.017 0.002 TYR 2 229 ARG 0.005 0.000 ARG 2 681 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 686 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 2 LYS cc_start: 0.4607 (tttt) cc_final: 0.4393 (tttt) REVERT: 1 309 ASP cc_start: 0.5970 (m-30) cc_final: 0.5677 (p0) REVERT: 1 368 ARG cc_start: 0.4294 (ptp-170) cc_final: 0.2943 (ttp-170) REVERT: 1 448 MET cc_start: 0.7933 (mtp) cc_final: 0.7684 (mtp) REVERT: 2 229 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.6553 (m-80) REVERT: 2 255 ASP cc_start: 0.6689 (m-30) cc_final: 0.6346 (t0) REVERT: 2 384 HIS cc_start: 0.6021 (OUTLIER) cc_final: 0.5616 (p-80) REVERT: 2 609 LYS cc_start: 0.7733 (mptt) cc_final: 0.7279 (mmtm) REVERT: 2 616 ASP cc_start: 0.7702 (m-30) cc_final: 0.7415 (m-30) REVERT: 2 713 ILE cc_start: 0.5837 (tp) cc_final: 0.5516 (tp) REVERT: 4 52 LYS cc_start: 0.5807 (mtmt) cc_final: 0.5383 (tptt) REVERT: 4 116 LYS cc_start: 0.8261 (mppt) cc_final: 0.8024 (mptt) REVERT: 4 176 LYS cc_start: 0.7243 (ttmm) cc_final: 0.6967 (tttt) REVERT: 5 177 LEU cc_start: 0.8250 (tt) cc_final: 0.8047 (tt) REVERT: 5 334 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7867 (mm-40) REVERT: 7 213 ASP cc_start: 0.7291 (p0) cc_final: 0.7040 (p0) REVERT: 7 358 GLN cc_start: 0.5432 (mt0) cc_final: 0.5211 (tp40) REVERT: 7 546 GLN cc_start: 0.6932 (tt0) cc_final: 0.6517 (tp40) REVERT: 7 558 TYR cc_start: 0.6548 (p90) cc_final: 0.6078 (p90) REVERT: 8 64 ILE cc_start: 0.7916 (mp) cc_final: 0.7702 (mp) REVERT: 8 292 ASN cc_start: 0.7537 (t0) cc_final: 0.6807 (t0) REVERT: 8 379 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7474 (mm-30) REVERT: 8 429 ARG cc_start: 0.8156 (ttt-90) cc_final: 0.7885 (ttt-90) REVERT: 9 122 GLN cc_start: 0.7498 (pm20) cc_final: 0.7202 (pm20) REVERT: 9 542 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7448 (tptt) REVERT: 9 553 ASN cc_start: 0.7817 (p0) cc_final: 0.6776 (t0) REVERT: 9 620 LEU cc_start: 0.8493 (mt) cc_final: 0.8227 (mt) outliers start: 8 outliers final: 3 residues processed: 691 average time/residue: 0.4586 time to fit residues: 485.5705 Evaluate side-chains 404 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 399 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 229 TYR Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 9 residue 9 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.8980 chunk 286 optimal weight: 1.9990 chunk 158 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 chunk 296 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 343 optimal weight: 0.1980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 HIS 1 325 GLN 1 386 ASN 1 489 HIS 2 12 HIS 2 44 ASN ** 2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 651 ASN 2 705 ASN 4 224 HIS 4 249 HIS 4 325 HIS 5 20 GLN 7 293 GLN 7 365 GLN ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 437 ASN ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 477 GLN 7 495 GLN 7 633 GLN 8 321 ASN 8 432 HIS 8 454 HIS 9 200 HIS 9 276 GLN 9 313 HIS 9 471 GLN 9 576 ASN 9 651 HIS 9 672 GLN 9 677 GLN 9 761 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30791 Z= 0.188 Angle : 0.593 7.783 41671 Z= 0.306 Chirality : 0.043 0.181 4749 Planarity : 0.004 0.059 5343 Dihedral : 5.122 51.460 4116 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.65 % Allowed : 13.26 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3766 helix: 0.69 (0.14), residues: 1319 sheet: -1.30 (0.16), residues: 947 loop : -2.65 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 322 HIS 0.015 0.001 HIS 5 128 PHE 0.019 0.002 PHE 2 574 TYR 0.021 0.001 TYR 7 141 ARG 0.005 0.000 ARG 8 469 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 430 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7456 (mt-10) REVERT: 1 2 LYS cc_start: 0.4691 (tttt) cc_final: 0.4461 (tttt) REVERT: 1 203 MET cc_start: 0.6710 (mtp) cc_final: 0.6468 (mtm) REVERT: 1 309 ASP cc_start: 0.5984 (m-30) cc_final: 0.5538 (p0) REVERT: 1 347 MET cc_start: 0.4192 (mtp) cc_final: 0.3709 (mtp) REVERT: 2 9 LYS cc_start: 0.7415 (tptp) cc_final: 0.7212 (mmmt) REVERT: 2 229 TYR cc_start: 0.7248 (m-80) cc_final: 0.7006 (m-80) REVERT: 2 255 ASP cc_start: 0.6959 (m-30) cc_final: 0.6619 (t0) REVERT: 2 282 LYS cc_start: 0.7917 (tmtt) cc_final: 0.7549 (ttmt) REVERT: 2 528 ASN cc_start: 0.6217 (m110) cc_final: 0.5819 (t0) REVERT: 2 616 ASP cc_start: 0.7688 (m-30) cc_final: 0.7386 (m-30) REVERT: 4 52 LYS cc_start: 0.5920 (mtmt) cc_final: 0.5452 (tptt) REVERT: 4 176 LYS cc_start: 0.7226 (ttmm) cc_final: 0.6950 (tttt) REVERT: 4 369 LYS cc_start: 0.8094 (mptt) cc_final: 0.7757 (mptt) REVERT: 4 417 MET cc_start: 0.5226 (ttp) cc_final: 0.4996 (ttm) REVERT: 7 438 ASP cc_start: 0.5519 (t0) cc_final: 0.5312 (t0) REVERT: 7 499 PHE cc_start: 0.5060 (p90) cc_final: 0.4840 (p90) REVERT: 7 546 GLN cc_start: 0.6798 (tt0) cc_final: 0.6453 (tp40) REVERT: 7 558 TYR cc_start: 0.6691 (p90) cc_final: 0.5806 (p90) REVERT: 8 292 ASN cc_start: 0.7457 (t0) cc_final: 0.6764 (t0) REVERT: 9 122 GLN cc_start: 0.7498 (pm20) cc_final: 0.7198 (pm20) REVERT: 9 309 ASN cc_start: 0.7189 (t0) cc_final: 0.6928 (t0) REVERT: 9 394 ASN cc_start: 0.7210 (m-40) cc_final: 0.6873 (m-40) REVERT: 9 542 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7486 (tptt) REVERT: 9 620 LEU cc_start: 0.8489 (mt) cc_final: 0.8251 (mt) outliers start: 55 outliers final: 32 residues processed: 469 average time/residue: 0.3917 time to fit residues: 296.6811 Evaluate side-chains 392 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 360 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 458 LYS Chi-restraints excluded: chain 2 residue 630 ASP Chi-restraints excluded: chain 2 residue 702 ILE Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 5 residue 151 GLN Chi-restraints excluded: chain 5 residue 159 ASN Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 5 residue 224 SER Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 507 ASN Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 581 SER Chi-restraints excluded: chain 7 residue 627 ASP Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 33 THR Chi-restraints excluded: chain 9 residue 104 CYS Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 382 ASP Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 782 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 343 optimal weight: 0.2980 chunk 371 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 384 HIS 4 163 HIS ** 4 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 385 GLN 5 205 GLN 7 273 ASN 7 283 HIS ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 322 HIS 8 484 HIS 9 310 ASN 9 313 HIS 9 811 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 30791 Z= 0.425 Angle : 0.697 11.216 41671 Z= 0.357 Chirality : 0.047 0.220 4749 Planarity : 0.005 0.060 5343 Dihedral : 5.323 46.845 4111 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.60 % Allowed : 15.93 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.13), residues: 3766 helix: 0.68 (0.14), residues: 1320 sheet: -1.11 (0.16), residues: 981 loop : -2.52 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 9 9 HIS 0.010 0.002 HIS 7 131 PHE 0.030 0.002 PHE 9 290 TYR 0.018 0.002 TYR 8 358 ARG 0.006 0.001 ARG 5 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 377 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7462 (mt-10) REVERT: 1 2 LYS cc_start: 0.4675 (tttt) cc_final: 0.4425 (tttp) REVERT: 1 368 ARG cc_start: 0.4329 (ptp-170) cc_final: 0.3132 (ttm110) REVERT: 2 9 LYS cc_start: 0.7514 (tptp) cc_final: 0.7287 (mmmt) REVERT: 2 528 ASN cc_start: 0.6313 (m110) cc_final: 0.5799 (t0) REVERT: 4 176 LYS cc_start: 0.7318 (ttmm) cc_final: 0.7032 (tttt) REVERT: 4 369 LYS cc_start: 0.8248 (mptt) cc_final: 0.7850 (mptt) REVERT: 4 417 MET cc_start: 0.5225 (ttp) cc_final: 0.5001 (ttm) REVERT: 5 88 LEU cc_start: 0.3966 (OUTLIER) cc_final: 0.3629 (pt) REVERT: 5 153 ARG cc_start: 0.7606 (mtp180) cc_final: 0.7112 (mtt180) REVERT: 5 201 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7305 (mp) REVERT: 5 236 LYS cc_start: 0.6965 (tttt) cc_final: 0.6729 (tttm) REVERT: 7 49 MET cc_start: 0.3925 (mmm) cc_final: 0.2812 (mpp) REVERT: 7 546 GLN cc_start: 0.6953 (tt0) cc_final: 0.6532 (tp40) REVERT: 8 292 ASN cc_start: 0.7589 (t0) cc_final: 0.6823 (t0) REVERT: 9 138 MET cc_start: 0.7841 (ptt) cc_final: 0.7596 (ptt) REVERT: 9 542 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7453 (tptt) REVERT: 9 553 ASN cc_start: 0.7785 (p0) cc_final: 0.6530 (t0) REVERT: 9 620 LEU cc_start: 0.8514 (mt) cc_final: 0.8239 (mt) outliers start: 120 outliers final: 73 residues processed: 471 average time/residue: 0.3910 time to fit residues: 299.3850 Evaluate side-chains 425 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 350 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 1 residue 86 ILE Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 578 LEU Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 165 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 520 LEU Chi-restraints excluded: chain 2 residue 702 ILE Chi-restraints excluded: chain 4 residue 47 ASP Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 173 MET Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 37 VAL Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 159 ASN Chi-restraints excluded: chain 5 residue 200 SER Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 5 residue 224 SER Chi-restraints excluded: chain 5 residue 258 SER Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 184 ILE Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 290 THR Chi-restraints excluded: chain 7 residue 297 VAL Chi-restraints excluded: chain 7 residue 300 ASP Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 507 ASN Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 542 THR Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 581 SER Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 7 residue 709 ILE Chi-restraints excluded: chain 8 residue 22 LEU Chi-restraints excluded: chain 8 residue 48 VAL Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 239 LYS Chi-restraints excluded: chain 8 residue 298 THR Chi-restraints excluded: chain 8 residue 483 ASP Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 33 THR Chi-restraints excluded: chain 9 residue 104 CYS Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 382 ASP Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 509 SER Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 782 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 1.9990 chunk 258 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 230 optimal weight: 0.5980 chunk 345 optimal weight: 0.6980 chunk 365 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 327 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 54 HIS ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 384 HIS 2 656 ASN ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30791 Z= 0.189 Angle : 0.564 9.103 41671 Z= 0.293 Chirality : 0.043 0.202 4749 Planarity : 0.004 0.060 5343 Dihedral : 4.928 46.070 4111 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.03 % Allowed : 17.70 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.14), residues: 3766 helix: 1.30 (0.14), residues: 1317 sheet: -0.92 (0.16), residues: 983 loop : -2.29 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 237 HIS 0.008 0.001 HIS 2 384 PHE 0.017 0.001 PHE 2 217 TYR 0.017 0.001 TYR 7 703 ARG 0.003 0.000 ARG 2 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 368 time to evaluate : 3.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7451 (mt-10) REVERT: 1 2 LYS cc_start: 0.4646 (tttt) cc_final: 0.4368 (tttp) REVERT: 1 32 TYR cc_start: 0.4888 (m-80) cc_final: 0.4599 (m-80) REVERT: 1 309 ASP cc_start: 0.5923 (OUTLIER) cc_final: 0.5498 (p0) REVERT: 1 368 ARG cc_start: 0.4338 (ptp-170) cc_final: 0.3182 (ttm110) REVERT: 1 429 ARG cc_start: 0.6777 (tpp-160) cc_final: 0.6511 (tpp80) REVERT: 2 9 LYS cc_start: 0.7466 (tptp) cc_final: 0.7221 (mmmt) REVERT: 2 528 ASN cc_start: 0.6262 (m110) cc_final: 0.5758 (t0) REVERT: 4 176 LYS cc_start: 0.7304 (ttmm) cc_final: 0.7011 (tttt) REVERT: 4 369 LYS cc_start: 0.8265 (mptt) cc_final: 0.7917 (mptt) REVERT: 4 390 ASP cc_start: 0.6117 (t0) cc_final: 0.5749 (t0) REVERT: 4 417 MET cc_start: 0.5202 (ttp) cc_final: 0.4957 (ttm) REVERT: 4 423 LYS cc_start: 0.7421 (mmtt) cc_final: 0.6795 (mttt) REVERT: 5 88 LEU cc_start: 0.3929 (OUTLIER) cc_final: 0.3479 (pt) REVERT: 5 236 LYS cc_start: 0.6783 (tttt) cc_final: 0.6524 (tttm) REVERT: 7 39 ASP cc_start: 0.5644 (t0) cc_final: 0.4587 (t0) REVERT: 7 546 GLN cc_start: 0.6821 (tt0) cc_final: 0.6592 (tp40) REVERT: 7 558 TYR cc_start: 0.6623 (p90) cc_final: 0.6104 (p90) REVERT: 8 292 ASN cc_start: 0.7439 (t0) cc_final: 0.6692 (t0) REVERT: 9 138 MET cc_start: 0.7822 (ptt) cc_final: 0.7572 (ptt) REVERT: 9 382 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: 9 542 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7470 (tptt) REVERT: 9 553 ASN cc_start: 0.7727 (p0) cc_final: 0.6367 (t0) REVERT: 9 620 LEU cc_start: 0.8471 (mt) cc_final: 0.8214 (mt) outliers start: 101 outliers final: 64 residues processed: 448 average time/residue: 0.4074 time to fit residues: 294.6410 Evaluate side-chains 416 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 349 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 1 residue 86 ILE Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 578 LEU Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 165 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 520 LEU Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 630 ASP Chi-restraints excluded: chain 4 residue 152 ASP Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 253 ASP Chi-restraints excluded: chain 5 residue 22 MET Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 159 ASN Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 200 SER Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 5 residue 224 SER Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 290 THR Chi-restraints excluded: chain 7 residue 297 VAL Chi-restraints excluded: chain 7 residue 300 ASP Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 462 GLU Chi-restraints excluded: chain 7 residue 507 ASN Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 298 THR Chi-restraints excluded: chain 8 residue 483 ASP Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 33 THR Chi-restraints excluded: chain 9 residue 76 ASP Chi-restraints excluded: chain 9 residue 104 CYS Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 382 ASP Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 481 MET Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 311 optimal weight: 0.6980 chunk 252 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 327 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 GLN 1 338 GLN 1 386 ASN ** 2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 384 HIS ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 310 ASN ** 9 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 778 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 30791 Z= 0.467 Angle : 0.709 11.230 41671 Z= 0.363 Chirality : 0.048 0.216 4749 Planarity : 0.005 0.058 5343 Dihedral : 5.340 48.132 4111 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.96 % Allowed : 18.36 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3766 helix: 0.83 (0.14), residues: 1320 sheet: -0.94 (0.17), residues: 987 loop : -2.36 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP 9 9 HIS 0.015 0.002 HIS 2 384 PHE 0.026 0.002 PHE 9 290 TYR 0.018 0.002 TYR 8 358 ARG 0.005 0.001 ARG 8 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 348 time to evaluate : 3.586 Fit side-chains revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7402 (mt-10) REVERT: 1 2 LYS cc_start: 0.4577 (tttt) cc_final: 0.4307 (tttp) REVERT: 1 32 TYR cc_start: 0.5380 (m-80) cc_final: 0.5060 (m-80) REVERT: 1 347 MET cc_start: 0.4189 (OUTLIER) cc_final: 0.3443 (mtp) REVERT: 1 368 ARG cc_start: 0.4384 (ptp-170) cc_final: 0.2759 (ttm110) REVERT: 1 488 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8892 (tp) REVERT: 2 9 LYS cc_start: 0.7719 (tptp) cc_final: 0.6668 (mmtp) REVERT: 2 528 ASN cc_start: 0.6188 (m110) cc_final: 0.5885 (t0) REVERT: 2 544 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7680 (tp) REVERT: 2 713 ILE cc_start: 0.6675 (tp) cc_final: 0.6189 (tp) REVERT: 4 52 LYS cc_start: 0.6699 (mtpp) cc_final: 0.5849 (tptt) REVERT: 4 176 LYS cc_start: 0.7359 (ttmm) cc_final: 0.7116 (tttt) REVERT: 4 369 LYS cc_start: 0.8330 (mptt) cc_final: 0.7879 (mptt) REVERT: 4 390 ASP cc_start: 0.6343 (t0) cc_final: 0.5955 (t0) REVERT: 4 417 MET cc_start: 0.5138 (ttp) cc_final: 0.4856 (ttm) REVERT: 4 423 LYS cc_start: 0.7524 (mmtt) cc_final: 0.6577 (mttt) REVERT: 5 57 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8100 (mt) REVERT: 5 88 LEU cc_start: 0.4125 (OUTLIER) cc_final: 0.3753 (pt) REVERT: 5 153 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7238 (mtt180) REVERT: 5 201 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7139 (mp) REVERT: 5 236 LYS cc_start: 0.7006 (tttt) cc_final: 0.6748 (tttm) REVERT: 7 364 GLN cc_start: 0.6613 (tp-100) cc_final: 0.5947 (pt0) REVERT: 8 292 ASN cc_start: 0.7617 (t0) cc_final: 0.7221 (t0) REVERT: 9 138 MET cc_start: 0.8076 (ptt) cc_final: 0.7829 (ptt) REVERT: 9 309 ASN cc_start: 0.7454 (t0) cc_final: 0.6868 (t0) REVERT: 9 542 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7461 (tptt) REVERT: 9 553 ASN cc_start: 0.7963 (p0) cc_final: 0.6794 (t0) REVERT: 9 620 LEU cc_start: 0.8452 (mt) cc_final: 0.8164 (mt) outliers start: 132 outliers final: 93 residues processed: 458 average time/residue: 0.3996 time to fit residues: 297.8754 Evaluate side-chains 432 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 333 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 1 residue 54 HIS Chi-restraints excluded: chain 1 residue 86 ILE Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 347 MET Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 387 THR Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 578 LEU Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 165 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 222 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 262 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 352 LEU Chi-restraints excluded: chain 2 residue 381 THR Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 520 LEU Chi-restraints excluded: chain 2 residue 533 VAL Chi-restraints excluded: chain 2 residue 544 LEU Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 4 residue 47 ASP Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 253 ASP Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 142 LEU Chi-restraints excluded: chain 5 residue 159 ASN Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 199 VAL Chi-restraints excluded: chain 5 residue 200 SER Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 5 residue 224 SER Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 208 LEU Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 290 THR Chi-restraints excluded: chain 7 residue 297 VAL Chi-restraints excluded: chain 7 residue 300 ASP Chi-restraints excluded: chain 7 residue 319 THR Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 413 VAL Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 456 LEU Chi-restraints excluded: chain 7 residue 462 GLU Chi-restraints excluded: chain 7 residue 507 ASN Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 542 THR Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 7 residue 683 LYS Chi-restraints excluded: chain 7 residue 709 ILE Chi-restraints excluded: chain 8 residue 48 VAL Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 166 LEU Chi-restraints excluded: chain 8 residue 203 THR Chi-restraints excluded: chain 8 residue 239 LYS Chi-restraints excluded: chain 8 residue 298 THR Chi-restraints excluded: chain 8 residue 367 THR Chi-restraints excluded: chain 8 residue 483 ASP Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 76 ASP Chi-restraints excluded: chain 9 residue 104 CYS Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 254 ILE Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 382 ASP Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 445 THR Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 0.0010 chunk 329 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 214 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 365 optimal weight: 0.6980 chunk 303 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 99 ASN 2 384 HIS 2 656 ASN 4 384 ASN ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 311 HIS 9 99 HIS 9 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30791 Z= 0.177 Angle : 0.559 9.600 41671 Z= 0.291 Chirality : 0.042 0.197 4749 Planarity : 0.004 0.057 5343 Dihedral : 4.885 45.586 4111 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.03 % Allowed : 19.38 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.14), residues: 3766 helix: 1.44 (0.14), residues: 1319 sheet: -0.76 (0.17), residues: 981 loop : -2.18 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 237 HIS 0.007 0.001 HIS 2 384 PHE 0.020 0.001 PHE 2 217 TYR 0.017 0.001 TYR 2 603 ARG 0.004 0.000 ARG 2 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 363 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7401 (mt-10) REVERT: 1 2 LYS cc_start: 0.4565 (tttt) cc_final: 0.4305 (tttp) REVERT: 1 32 TYR cc_start: 0.5203 (m-80) cc_final: 0.4963 (m-80) REVERT: 1 203 MET cc_start: 0.5805 (OUTLIER) cc_final: 0.5021 (mtm) REVERT: 1 326 MET cc_start: 0.6267 (mmm) cc_final: 0.5949 (mmt) REVERT: 1 368 ARG cc_start: 0.4459 (ptp-170) cc_final: 0.2859 (ttm110) REVERT: 1 429 ARG cc_start: 0.6768 (tpp-160) cc_final: 0.6531 (tpp80) REVERT: 2 528 ASN cc_start: 0.6105 (m110) cc_final: 0.5750 (t0) REVERT: 2 713 ILE cc_start: 0.6484 (tp) cc_final: 0.5994 (tp) REVERT: 4 52 LYS cc_start: 0.6639 (mtpp) cc_final: 0.5754 (tptt) REVERT: 4 176 LYS cc_start: 0.7295 (ttmm) cc_final: 0.7005 (tttt) REVERT: 4 369 LYS cc_start: 0.8339 (mptt) cc_final: 0.7909 (mptt) REVERT: 4 390 ASP cc_start: 0.6048 (t0) cc_final: 0.5675 (t0) REVERT: 4 423 LYS cc_start: 0.7479 (mmtt) cc_final: 0.6705 (mttt) REVERT: 5 57 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8175 (mt) REVERT: 5 88 LEU cc_start: 0.3857 (OUTLIER) cc_final: 0.3391 (pt) REVERT: 5 236 LYS cc_start: 0.6821 (tttt) cc_final: 0.6553 (tttm) REVERT: 7 49 MET cc_start: 0.3405 (mmm) cc_final: 0.2413 (mpp) REVERT: 7 438 ASP cc_start: 0.5759 (t0) cc_final: 0.5556 (t0) REVERT: 8 292 ASN cc_start: 0.7491 (t0) cc_final: 0.6993 (t0) REVERT: 8 326 ASP cc_start: 0.7836 (t0) cc_final: 0.7631 (t0) REVERT: 9 138 MET cc_start: 0.7895 (ptt) cc_final: 0.7688 (ptt) REVERT: 9 381 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7271 (mt) REVERT: 9 542 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7458 (tptt) REVERT: 9 553 ASN cc_start: 0.7801 (p0) cc_final: 0.6501 (t0) outliers start: 101 outliers final: 70 residues processed: 444 average time/residue: 0.4004 time to fit residues: 288.3708 Evaluate side-chains 420 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 346 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 86 ILE Chi-restraints excluded: chain 1 residue 203 MET Chi-restraints excluded: chain 1 residue 286 ILE Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 367 ILE Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 578 LEU Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 165 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 352 LEU Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 483 MET Chi-restraints excluded: chain 2 residue 520 LEU Chi-restraints excluded: chain 2 residue 544 LEU Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 253 ASP Chi-restraints excluded: chain 4 residue 278 MET Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 142 LEU Chi-restraints excluded: chain 5 residue 159 ASN Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 200 SER Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 208 LEU Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 290 THR Chi-restraints excluded: chain 7 residue 300 ASP Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 507 ASN Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 8 residue 127 THR Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 298 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 76 ASP Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 351 ASP Chi-restraints excluded: chain 9 residue 381 LEU Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 445 THR Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 706 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 267 optimal weight: 0.7980 chunk 206 optimal weight: 10.0000 chunk 307 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 364 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 12 HIS 2 384 HIS ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 546 GLN 9 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30791 Z= 0.191 Angle : 0.555 9.898 41671 Z= 0.286 Chirality : 0.043 0.191 4749 Planarity : 0.004 0.055 5343 Dihedral : 4.770 45.269 4111 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.27 % Allowed : 19.56 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.14), residues: 3766 helix: 1.60 (0.14), residues: 1320 sheet: -0.64 (0.17), residues: 976 loop : -2.13 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 237 HIS 0.009 0.001 HIS 2 384 PHE 0.019 0.001 PHE 9 476 TYR 0.023 0.001 TYR 2 603 ARG 0.004 0.000 ARG 2 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 363 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7388 (mt-10) REVERT: 1 2 LYS cc_start: 0.4625 (tttt) cc_final: 0.4366 (tttp) REVERT: 1 32 TYR cc_start: 0.5192 (m-80) cc_final: 0.4984 (m-80) REVERT: 1 47 ARG cc_start: 0.6628 (mtm-85) cc_final: 0.5781 (mtp85) REVERT: 1 203 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.4969 (mtm) REVERT: 1 326 MET cc_start: 0.6312 (mmm) cc_final: 0.6038 (mmt) REVERT: 1 368 ARG cc_start: 0.4425 (ptp-170) cc_final: 0.2829 (ttm110) REVERT: 1 429 ARG cc_start: 0.6775 (tpp-160) cc_final: 0.6525 (tpp80) REVERT: 2 384 HIS cc_start: 0.6470 (OUTLIER) cc_final: 0.5590 (m90) REVERT: 2 528 ASN cc_start: 0.6110 (m110) cc_final: 0.5745 (t0) REVERT: 2 544 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7371 (tp) REVERT: 2 713 ILE cc_start: 0.6490 (tp) cc_final: 0.6001 (tp) REVERT: 4 52 LYS cc_start: 0.6635 (mtpp) cc_final: 0.5750 (tptt) REVERT: 4 176 LYS cc_start: 0.7171 (ttmm) cc_final: 0.6881 (tttt) REVERT: 4 369 LYS cc_start: 0.8377 (mptt) cc_final: 0.7960 (mptt) REVERT: 4 390 ASP cc_start: 0.6038 (t0) cc_final: 0.5651 (t0) REVERT: 4 423 LYS cc_start: 0.7555 (mmtt) cc_final: 0.6732 (mttt) REVERT: 5 57 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8176 (mt) REVERT: 5 88 LEU cc_start: 0.3923 (OUTLIER) cc_final: 0.3465 (pt) REVERT: 5 236 LYS cc_start: 0.6831 (tttt) cc_final: 0.6543 (tttp) REVERT: 5 260 ASN cc_start: 0.6594 (t0) cc_final: 0.6241 (t0) REVERT: 7 49 MET cc_start: 0.3500 (mmm) cc_final: 0.2481 (mpp) REVERT: 7 438 ASP cc_start: 0.5696 (t0) cc_final: 0.5452 (t0) REVERT: 8 292 ASN cc_start: 0.7497 (t0) cc_final: 0.6992 (t0) REVERT: 9 381 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7311 (mt) REVERT: 9 542 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7344 (tptt) REVERT: 9 553 ASN cc_start: 0.7745 (p0) cc_final: 0.6461 (t0) REVERT: 9 657 ILE cc_start: 0.8637 (mm) cc_final: 0.8393 (mm) outliers start: 109 outliers final: 85 residues processed: 457 average time/residue: 0.3933 time to fit residues: 293.2311 Evaluate side-chains 438 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 347 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 86 ILE Chi-restraints excluded: chain 1 residue 203 MET Chi-restraints excluded: chain 1 residue 286 ILE Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 367 ILE Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 578 LEU Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 165 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 262 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 352 LEU Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 520 LEU Chi-restraints excluded: chain 2 residue 533 VAL Chi-restraints excluded: chain 2 residue 544 LEU Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 4 residue 47 ASP Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 253 ASP Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 5 residue 142 LEU Chi-restraints excluded: chain 5 residue 159 ASN Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 200 SER Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 7 residue 36 VAL Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 208 LEU Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 290 THR Chi-restraints excluded: chain 7 residue 297 VAL Chi-restraints excluded: chain 7 residue 300 ASP Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 456 LEU Chi-restraints excluded: chain 7 residue 462 GLU Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 542 THR Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 8 residue 48 VAL Chi-restraints excluded: chain 8 residue 127 THR Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 162 ASN Chi-restraints excluded: chain 8 residue 166 LEU Chi-restraints excluded: chain 8 residue 203 THR Chi-restraints excluded: chain 8 residue 239 LYS Chi-restraints excluded: chain 8 residue 298 THR Chi-restraints excluded: chain 8 residue 367 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 76 ASP Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 254 ILE Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 381 LEU Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 706 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 286 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 384 HIS ** 2 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 547 ASN ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30791 Z= 0.278 Angle : 0.589 10.235 41671 Z= 0.302 Chirality : 0.044 0.188 4749 Planarity : 0.004 0.055 5343 Dihedral : 4.850 46.159 4111 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.75 % Allowed : 19.38 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.14), residues: 3766 helix: 1.54 (0.14), residues: 1318 sheet: -0.65 (0.17), residues: 974 loop : -2.10 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 9 9 HIS 0.008 0.001 HIS 7 635 PHE 0.020 0.002 PHE 2 41 TYR 0.023 0.002 TYR 2 603 ARG 0.005 0.000 ARG 2 712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 352 time to evaluate : 3.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7418 (mt-10) REVERT: 1 2 LYS cc_start: 0.4711 (tttt) cc_final: 0.4419 (tttp) REVERT: 1 203 MET cc_start: 0.5630 (OUTLIER) cc_final: 0.4833 (mtm) REVERT: 1 326 MET cc_start: 0.6417 (mmm) cc_final: 0.6170 (mmt) REVERT: 1 347 MET cc_start: 0.3840 (OUTLIER) cc_final: 0.3128 (mtp) REVERT: 1 368 ARG cc_start: 0.4032 (ptp-170) cc_final: 0.2416 (ttm110) REVERT: 1 429 ARG cc_start: 0.6821 (tpp-160) cc_final: 0.6563 (tpp80) REVERT: 2 384 HIS cc_start: 0.6583 (OUTLIER) cc_final: 0.5581 (m90) REVERT: 2 528 ASN cc_start: 0.6221 (m110) cc_final: 0.5815 (t0) REVERT: 2 713 ILE cc_start: 0.6559 (tp) cc_final: 0.6022 (tp) REVERT: 4 52 LYS cc_start: 0.6636 (mtpp) cc_final: 0.5772 (tptt) REVERT: 4 176 LYS cc_start: 0.7159 (ttmm) cc_final: 0.6933 (tttt) REVERT: 4 369 LYS cc_start: 0.8350 (mptt) cc_final: 0.7930 (mptt) REVERT: 4 390 ASP cc_start: 0.6165 (t0) cc_final: 0.5768 (t0) REVERT: 4 423 LYS cc_start: 0.7584 (mmtt) cc_final: 0.6777 (mttt) REVERT: 5 57 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8141 (mt) REVERT: 5 88 LEU cc_start: 0.3940 (OUTLIER) cc_final: 0.3504 (pt) REVERT: 5 236 LYS cc_start: 0.6880 (tttt) cc_final: 0.6585 (tttp) REVERT: 5 260 ASN cc_start: 0.6603 (t0) cc_final: 0.6251 (t0) REVERT: 7 49 MET cc_start: 0.3736 (mmm) cc_final: 0.3186 (mpp) REVERT: 8 26 MET cc_start: 0.7144 (ptm) cc_final: 0.6868 (ptt) REVERT: 8 292 ASN cc_start: 0.7539 (t0) cc_final: 0.7052 (t0) REVERT: 9 381 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7286 (mt) REVERT: 9 542 LYS cc_start: 0.7813 (mmmt) cc_final: 0.7343 (tptt) REVERT: 9 553 ASN cc_start: 0.7796 (p0) cc_final: 0.6534 (t0) outliers start: 125 outliers final: 104 residues processed: 457 average time/residue: 0.3975 time to fit residues: 295.1306 Evaluate side-chains 453 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 343 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 1 residue 54 HIS Chi-restraints excluded: chain 1 residue 86 ILE Chi-restraints excluded: chain 1 residue 203 MET Chi-restraints excluded: chain 1 residue 286 ILE Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 347 MET Chi-restraints excluded: chain 1 residue 367 ILE Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 78 LEU Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 165 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 222 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 262 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 311 ASP Chi-restraints excluded: chain 2 residue 352 LEU Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 520 LEU Chi-restraints excluded: chain 2 residue 533 VAL Chi-restraints excluded: chain 2 residue 544 LEU Chi-restraints excluded: chain 2 residue 610 LEU Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 4 residue 47 ASP Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 174 LEU Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 253 ASP Chi-restraints excluded: chain 4 residue 278 MET Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 5 residue 142 LEU Chi-restraints excluded: chain 5 residue 159 ASN Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 165 ASN Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 200 SER Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 208 LEU Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 290 THR Chi-restraints excluded: chain 7 residue 297 VAL Chi-restraints excluded: chain 7 residue 300 ASP Chi-restraints excluded: chain 7 residue 319 THR Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 413 VAL Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 456 LEU Chi-restraints excluded: chain 7 residue 507 ASN Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 542 THR Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 623 VAL Chi-restraints excluded: chain 7 residue 627 ASP Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 8 residue 48 VAL Chi-restraints excluded: chain 8 residue 127 THR Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 162 ASN Chi-restraints excluded: chain 8 residue 166 LEU Chi-restraints excluded: chain 8 residue 203 THR Chi-restraints excluded: chain 8 residue 239 LYS Chi-restraints excluded: chain 8 residue 298 THR Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 367 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 76 ASP Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 254 ILE Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 296 VAL Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 381 LEU Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 692 LEU Chi-restraints excluded: chain 9 residue 706 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 0.6980 chunk 349 optimal weight: 0.9990 chunk 318 optimal weight: 0.0980 chunk 339 optimal weight: 5.9990 chunk 348 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 306 optimal weight: 0.5980 chunk 321 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 291 GLN 2 384 HIS ** 2 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 384 ASN ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 547 ASN 9 155 GLN ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30791 Z= 0.164 Angle : 0.547 10.185 41671 Z= 0.281 Chirality : 0.042 0.223 4749 Planarity : 0.004 0.055 5343 Dihedral : 4.670 45.488 4111 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.21 % Allowed : 19.92 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.14), residues: 3766 helix: 1.79 (0.14), residues: 1320 sheet: -0.57 (0.17), residues: 978 loop : -2.02 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 237 HIS 0.014 0.001 HIS 2 384 PHE 0.019 0.001 PHE 1 26 TYR 0.023 0.001 TYR 2 603 ARG 0.004 0.000 ARG 2 712 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 359 time to evaluate : 3.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7380 (mt-10) REVERT: 1 2 LYS cc_start: 0.4701 (tttt) cc_final: 0.4423 (tttp) REVERT: 1 47 ARG cc_start: 0.6601 (mtm-85) cc_final: 0.5865 (mtp85) REVERT: 1 203 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.4957 (mtm) REVERT: 1 326 MET cc_start: 0.6426 (mmm) cc_final: 0.6185 (mmt) REVERT: 1 354 GLU cc_start: 0.5348 (tm-30) cc_final: 0.5120 (tm-30) REVERT: 1 368 ARG cc_start: 0.3959 (ptp-170) cc_final: 0.2359 (ttm110) REVERT: 1 429 ARG cc_start: 0.6771 (tpp-160) cc_final: 0.6529 (tpp80) REVERT: 2 384 HIS cc_start: 0.6378 (OUTLIER) cc_final: 0.5588 (m90) REVERT: 2 528 ASN cc_start: 0.6177 (m110) cc_final: 0.5792 (t0) REVERT: 2 703 ARG cc_start: 0.8051 (mtm180) cc_final: 0.7766 (mtm180) REVERT: 2 713 ILE cc_start: 0.6527 (tp) cc_final: 0.5997 (tp) REVERT: 4 52 LYS cc_start: 0.6492 (mtpp) cc_final: 0.5706 (tptt) REVERT: 4 72 VAL cc_start: 0.7114 (t) cc_final: 0.6827 (p) REVERT: 4 176 LYS cc_start: 0.7056 (ttmm) cc_final: 0.6781 (tttt) REVERT: 4 369 LYS cc_start: 0.8390 (mptt) cc_final: 0.8003 (mptt) REVERT: 4 390 ASP cc_start: 0.5867 (t0) cc_final: 0.5491 (t0) REVERT: 4 423 LYS cc_start: 0.7563 (mmtt) cc_final: 0.6750 (mttt) REVERT: 5 57 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8151 (mt) REVERT: 5 88 LEU cc_start: 0.3751 (OUTLIER) cc_final: 0.3266 (pt) REVERT: 5 236 LYS cc_start: 0.6850 (tttt) cc_final: 0.6484 (tttm) REVERT: 5 260 ASN cc_start: 0.6586 (t0) cc_final: 0.6230 (t0) REVERT: 7 49 MET cc_start: 0.3658 (mmm) cc_final: 0.2619 (mpp) REVERT: 8 292 ASN cc_start: 0.7440 (t0) cc_final: 0.6928 (t0) REVERT: 9 381 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7281 (mt) REVERT: 9 542 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7326 (tptt) REVERT: 9 553 ASN cc_start: 0.7683 (p0) cc_final: 0.6386 (t0) REVERT: 9 657 ILE cc_start: 0.8606 (mm) cc_final: 0.8367 (mm) outliers start: 107 outliers final: 93 residues processed: 447 average time/residue: 0.4024 time to fit residues: 290.9275 Evaluate side-chains 442 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 344 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 1 residue 86 ILE Chi-restraints excluded: chain 1 residue 203 MET Chi-restraints excluded: chain 1 residue 232 ASP Chi-restraints excluded: chain 1 residue 286 ILE Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 367 ILE Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 387 THR Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 165 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 222 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 262 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 352 LEU Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 458 LYS Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 520 LEU Chi-restraints excluded: chain 2 residue 533 VAL Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 253 ASP Chi-restraints excluded: chain 4 residue 278 MET Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 4 residue 384 ASN Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 5 residue 142 LEU Chi-restraints excluded: chain 5 residue 159 ASN Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 165 ASN Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 200 SER Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 5 residue 258 SER Chi-restraints excluded: chain 7 residue 127 TYR Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 290 THR Chi-restraints excluded: chain 7 residue 297 VAL Chi-restraints excluded: chain 7 residue 300 ASP Chi-restraints excluded: chain 7 residue 319 THR Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 413 VAL Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 456 LEU Chi-restraints excluded: chain 7 residue 462 GLU Chi-restraints excluded: chain 7 residue 507 ASN Chi-restraints excluded: chain 7 residue 542 THR Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 7 residue 683 LYS Chi-restraints excluded: chain 8 residue 48 VAL Chi-restraints excluded: chain 8 residue 127 THR Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 162 ASN Chi-restraints excluded: chain 8 residue 203 THR Chi-restraints excluded: chain 8 residue 298 THR Chi-restraints excluded: chain 8 residue 367 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 76 ASP Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 254 ILE Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 296 VAL Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 381 LEU Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 692 LEU Chi-restraints excluded: chain 9 residue 706 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 359 optimal weight: 0.4980 chunk 219 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 376 optimal weight: 0.7980 chunk 346 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 384 HIS ** 2 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 547 ASN 9 155 GLN ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 308 HIS ** 9 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 30791 Z= 0.248 Angle : 0.578 10.854 41671 Z= 0.297 Chirality : 0.043 0.271 4749 Planarity : 0.004 0.055 5343 Dihedral : 4.725 45.771 4111 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 3.15 % Allowed : 20.34 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.14), residues: 3766 helix: 1.73 (0.14), residues: 1319 sheet: -0.54 (0.17), residues: 964 loop : -2.01 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 237 HIS 0.005 0.001 HIS 7 635 PHE 0.019 0.001 PHE 2 41 TYR 0.024 0.001 TYR 2 603 ARG 0.005 0.000 ARG 2 712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 347 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7426 (mt-10) REVERT: 1 2 LYS cc_start: 0.4647 (tttt) cc_final: 0.4383 (tttp) REVERT: 1 47 ARG cc_start: 0.6674 (mtm-85) cc_final: 0.5942 (mtp85) REVERT: 1 203 MET cc_start: 0.5667 (OUTLIER) cc_final: 0.4885 (mtm) REVERT: 1 326 MET cc_start: 0.6438 (mmm) cc_final: 0.6216 (mmt) REVERT: 1 354 GLU cc_start: 0.5449 (tm-30) cc_final: 0.5222 (tm-30) REVERT: 1 368 ARG cc_start: 0.4028 (ptp-170) cc_final: 0.2370 (ttm110) REVERT: 1 429 ARG cc_start: 0.6803 (tpp-160) cc_final: 0.6540 (tpp80) REVERT: 2 384 HIS cc_start: 0.6537 (OUTLIER) cc_final: 0.5613 (m90) REVERT: 2 528 ASN cc_start: 0.6313 (m110) cc_final: 0.5934 (t0) REVERT: 2 703 ARG cc_start: 0.8076 (mtm180) cc_final: 0.7792 (mtm180) REVERT: 2 713 ILE cc_start: 0.6544 (tp) cc_final: 0.6005 (tp) REVERT: 4 52 LYS cc_start: 0.6578 (mtpp) cc_final: 0.5709 (tptt) REVERT: 4 72 VAL cc_start: 0.7171 (t) cc_final: 0.6867 (p) REVERT: 4 176 LYS cc_start: 0.7045 (ttmm) cc_final: 0.6811 (tttt) REVERT: 4 369 LYS cc_start: 0.8399 (mptt) cc_final: 0.7978 (mptt) REVERT: 4 384 ASN cc_start: 0.6753 (OUTLIER) cc_final: 0.6008 (t0) REVERT: 4 390 ASP cc_start: 0.6031 (t0) cc_final: 0.5634 (t0) REVERT: 4 423 LYS cc_start: 0.7600 (mmtt) cc_final: 0.6970 (mttt) REVERT: 5 57 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8137 (mt) REVERT: 5 88 LEU cc_start: 0.3962 (OUTLIER) cc_final: 0.3502 (pt) REVERT: 5 236 LYS cc_start: 0.6879 (tttt) cc_final: 0.6600 (tttp) REVERT: 5 260 ASN cc_start: 0.6586 (t0) cc_final: 0.6223 (t0) REVERT: 7 504 ARG cc_start: 0.7204 (mmp-170) cc_final: 0.6868 (mmm160) REVERT: 8 292 ASN cc_start: 0.7532 (t0) cc_final: 0.7026 (t0) REVERT: 9 381 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7256 (mt) REVERT: 9 542 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7321 (tptt) REVERT: 9 553 ASN cc_start: 0.7716 (p0) cc_final: 0.6448 (t0) outliers start: 105 outliers final: 91 residues processed: 438 average time/residue: 0.4118 time to fit residues: 291.9830 Evaluate side-chains 439 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 342 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 86 ILE Chi-restraints excluded: chain 1 residue 203 MET Chi-restraints excluded: chain 1 residue 286 ILE Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 367 ILE Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 387 THR Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 165 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 222 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 262 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 311 ASP Chi-restraints excluded: chain 2 residue 352 LEU Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 520 LEU Chi-restraints excluded: chain 2 residue 533 VAL Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 229 LEU Chi-restraints excluded: chain 4 residue 253 ASP Chi-restraints excluded: chain 4 residue 278 MET Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 4 residue 384 ASN Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 5 residue 142 LEU Chi-restraints excluded: chain 5 residue 159 ASN Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 165 ASN Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 200 SER Chi-restraints excluded: chain 5 residue 258 SER Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 290 THR Chi-restraints excluded: chain 7 residue 297 VAL Chi-restraints excluded: chain 7 residue 300 ASP Chi-restraints excluded: chain 7 residue 319 THR Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 413 VAL Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 456 LEU Chi-restraints excluded: chain 7 residue 507 ASN Chi-restraints excluded: chain 7 residue 542 THR Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 623 VAL Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 7 residue 683 LYS Chi-restraints excluded: chain 8 residue 48 VAL Chi-restraints excluded: chain 8 residue 127 THR Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 162 ASN Chi-restraints excluded: chain 8 residue 203 THR Chi-restraints excluded: chain 8 residue 298 THR Chi-restraints excluded: chain 8 residue 367 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 76 ASP Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 254 ILE Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 296 VAL Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 381 LEU Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 692 LEU Chi-restraints excluded: chain 9 residue 706 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 319 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 276 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 300 optimal weight: 0.3980 chunk 125 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 359 HIS 2 384 HIS 2 656 ASN 2 664 ASN 4 384 ASN ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 495 GLN 7 547 ASN 9 155 GLN ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.194186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147160 restraints weight = 40503.767| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.87 r_work: 0.3609 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 30791 Z= 0.176 Angle : 0.549 10.527 41671 Z= 0.283 Chirality : 0.042 0.237 4749 Planarity : 0.004 0.054 5343 Dihedral : 4.526 45.771 4108 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.15 % Favored : 94.82 % Rotamer: Outliers : 3.21 % Allowed : 20.46 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.14), residues: 3766 helix: 1.87 (0.14), residues: 1322 sheet: -0.51 (0.17), residues: 971 loop : -1.95 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 237 HIS 0.007 0.001 HIS 2 384 PHE 0.019 0.001 PHE 7 499 TYR 0.032 0.001 TYR 2 603 ARG 0.004 0.000 ARG 2 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7646.89 seconds wall clock time: 138 minutes 41.84 seconds (8321.84 seconds total)