Starting phenix.real_space_refine on Wed Feb 21 05:35:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/02_2024/7w9b_32363.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/02_2024/7w9b_32363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/02_2024/7w9b_32363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/02_2024/7w9b_32363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/02_2024/7w9b_32363.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/02_2024/7w9b_32363.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 18970 2.51 5 N 4982 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 198": "OD1" <-> "OD2" Residue "D ASP 228": "OD1" <-> "OD2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 389": "OD1" <-> "OD2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 428": "OD1" <-> "OD2" Residue "D ASP 442": "OD1" <-> "OD2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 571": "OD1" <-> "OD2" Residue "D ASP 586": "OD1" <-> "OD2" Residue "D PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 979": "OD1" <-> "OD2" Residue "D TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1127": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29737 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "C" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "D" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Time building chain proxies: 15.00, per 1000 atoms: 0.50 Number of scatterers: 29737 At special positions: 0 Unit cell: (156.299, 171.601, 241.553, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 143 16.00 O 5642 8.00 N 4982 7.00 C 18970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 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: 11.02 Conformation dependent library (CDL) restraints added in 5.2 seconds 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7076 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 49 sheets defined 30.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.733A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.440A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.512A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.891A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.556A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.526A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.802A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.532A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.679A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.776A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.833A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.733A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.623A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.574A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.571A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.727A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.711A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.618A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.552A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 3.679A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 53 removed outlier: 3.887A pdb=" N ALA A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 4.287A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.645A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.561A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.533A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix removed outlier: 3.715A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.736A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.001A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.607A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.945A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.521A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.923A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.524A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.608A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.052A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.718A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.824A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.518A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.607A pdb=" N ASN A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.875A pdb=" N THR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.141A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.818A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.463A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.766A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.546A pdb=" N ASN D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.627A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.761A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.596A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 780 removed outlier: 3.512A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 773 " --> pdb=" O GLY D 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.642A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.541A pdb=" N GLN D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR D 873 " --> pdb=" O MET D 869 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 883 " --> pdb=" O ALA D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 891 removed outlier: 4.079A pdb=" N GLY D 891 " --> pdb=" O PHE D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.840A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.605A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.573A pdb=" N ASN D 950 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.675A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D1002 " --> pdb=" O THR D 998 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D1016 " --> pdb=" O LEU D1012 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D1030 " --> pdb=" O ALA D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1147 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.987A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.039A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.627A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.457A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.202A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.015A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.403A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.359A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'B' and resid 721 through 722 Processing sheet with id=AB6, first strand: chain 'B' and resid 721 through 722 removed outlier: 3.784A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.793A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.688A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.501A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.681A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.231A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.543A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.549A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.365A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AD2, first strand: chain 'C' and resid 717 through 722 removed outlier: 6.922A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.596A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AD5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'A' and resid 131 through 134 removed outlier: 6.013A pdb=" N GLU A 140 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.252A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.966A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.601A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.838A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.847A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.343A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 324 through 327 removed outlier: 4.043A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.614A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'D' and resid 654 through 660 removed outlier: 6.283A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 673 " --> pdb=" O ILE D 693 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.690A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.803A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'D' and resid 1120 through 1122 1146 hydrogen bonds defined for protein. 3177 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: 12.19 Time building geometry restraints manager: 12.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9636 1.35 - 1.47: 7670 1.47 - 1.60: 12944 1.60 - 1.72: 0 1.72 - 1.84: 194 Bond restraints: 30444 Sorted by residual: bond pdb=" C PHE B 497 " pdb=" N GLN B 498 " ideal model delta sigma weight residual 1.327 1.358 -0.031 1.71e-02 3.42e+03 3.30e+00 bond pdb=" N SER A 19 " pdb=" CA SER A 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N GLN C 14 " pdb=" CA GLN C 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLN B 14 " pdb=" CA GLN B 14 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" N GLN D 14 " pdb=" CA GLN D 14 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 ... (remaining 30439 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.41: 825 106.41 - 113.33: 16212 113.33 - 120.25: 10460 120.25 - 127.16: 13562 127.16 - 134.08: 337 Bond angle restraints: 41396 Sorted by residual: angle pdb=" N ILE B 410 " pdb=" CA ILE B 410 " pdb=" C ILE B 410 " ideal model delta sigma weight residual 106.21 109.52 -3.31 1.07e+00 8.73e-01 9.57e+00 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 112.12 109.54 2.58 8.40e-01 1.42e+00 9.42e+00 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.46 126.27 -3.81 1.41e+00 5.03e-01 7.29e+00 angle pdb=" C LEU B 916 " pdb=" CA LEU B 916 " pdb=" CB LEU B 916 " ideal model delta sigma weight residual 110.96 107.45 3.51 1.54e+00 4.22e-01 5.20e+00 angle pdb=" C GLU A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta sigma weight residual 127.00 132.42 -5.42 2.40e+00 1.74e-01 5.11e+00 ... (remaining 41391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 16876 17.80 - 35.59: 1022 35.59 - 53.39: 163 53.39 - 71.18: 54 71.18 - 88.98: 21 Dihedral angle restraints: 18136 sinusoidal: 7139 harmonic: 10997 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -125.67 39.67 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual -86.00 -47.04 -38.96 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 127.72 -34.72 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 18133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3303 0.037 - 0.074: 899 0.074 - 0.112: 290 0.112 - 0.149: 120 0.149 - 0.186: 4 Chirality restraints: 4616 Sorted by residual: chirality pdb=" CA ILE D 896 " pdb=" N ILE D 896 " pdb=" C ILE D 896 " pdb=" CB ILE D 896 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA ILE C 896 " pdb=" N ILE C 896 " pdb=" C ILE C 896 " pdb=" CB ILE C 896 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA ILE D 714 " pdb=" N ILE D 714 " pdb=" C ILE D 714 " pdb=" CB ILE D 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 4613 not shown) Planarity restraints: 5375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D1068 " -0.023 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO D1069 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO D1069 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D1069 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 896 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO D 897 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 897 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 897 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO B 521 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.018 5.00e-02 4.00e+02 ... (remaining 5372 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 292 2.63 - 3.19: 25876 3.19 - 3.76: 43714 3.76 - 4.33: 63049 4.33 - 4.90: 103930 Nonbonded interactions: 236861 Sorted by model distance: nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.057 2.440 nonbonded pdb=" OG1 THR B 883 " pdb=" OH TYR C 707 " model vdw 2.058 2.440 nonbonded pdb=" O GLN C 755 " pdb=" OG SER D 968 " model vdw 2.064 2.440 nonbonded pdb=" O GLN B 755 " pdb=" OG SER C 968 " model vdw 2.077 2.440 nonbonded pdb=" OE1 GLN B 965 " pdb=" OG SER B1003 " model vdw 2.131 2.440 ... (remaining 236856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 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: 11.230 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 75.400 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.150 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30444 Z= 0.239 Angle : 0.582 6.493 41396 Z= 0.325 Chirality : 0.042 0.186 4616 Planarity : 0.003 0.034 5375 Dihedral : 12.343 88.980 10934 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.03 % Allowed : 1.27 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -3.40 (0.11), residues: 3733 helix: -2.50 (0.11), residues: 1023 sheet: -2.08 (0.17), residues: 643 loop : -2.18 (0.11), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 203 HIS 0.004 0.001 HIS A 540 PHE 0.011 0.001 PHE C1075 TYR 0.014 0.001 TYR D 707 ARG 0.003 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 762 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 TRP cc_start: 0.7580 (m-90) cc_final: 0.7314 (m-90) REVERT: B 118 LEU cc_start: 0.8635 (tp) cc_final: 0.8372 (tp) REVERT: B 133 PHE cc_start: 0.7302 (m-80) cc_final: 0.6507 (m-80) REVERT: B 140 PHE cc_start: 0.6176 (p90) cc_final: 0.5897 (p90) REVERT: B 191 GLU cc_start: 0.8119 (tt0) cc_final: 0.7717 (tp30) REVERT: B 202 LYS cc_start: 0.7441 (mttt) cc_final: 0.7082 (mtpp) REVERT: B 317 ASN cc_start: 0.7107 (m-40) cc_final: 0.6738 (m110) REVERT: B 398 ASP cc_start: 0.3477 (m-30) cc_final: 0.2261 (m-30) REVERT: B 541 PHE cc_start: 0.6590 (m-80) cc_final: 0.6298 (m-80) REVERT: B 546 LEU cc_start: 0.5887 (mm) cc_final: 0.5666 (tp) REVERT: B 559 PHE cc_start: 0.6082 (p90) cc_final: 0.5537 (p90) REVERT: B 568 ASP cc_start: 0.7517 (p0) cc_final: 0.6925 (p0) REVERT: B 574 ASP cc_start: 0.8324 (t70) cc_final: 0.8005 (m-30) REVERT: C 36 VAL cc_start: 0.8669 (t) cc_final: 0.8305 (m) REVERT: C 129 LYS cc_start: 0.7686 (mttt) cc_final: 0.7354 (mtpp) REVERT: C 238 PHE cc_start: 0.7867 (p90) cc_final: 0.7411 (p90) REVERT: C 584 ILE cc_start: 0.8435 (mt) cc_final: 0.8231 (mt) REVERT: A 35 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7619 (mt-10) REVERT: A 64 ASN cc_start: 0.7388 (m-40) cc_final: 0.6982 (t0) REVERT: A 82 MET cc_start: 0.6887 (mmm) cc_final: 0.6660 (mmt) REVERT: A 322 ASN cc_start: 0.5444 (p0) cc_final: 0.4737 (t0) REVERT: A 457 GLU cc_start: 0.3631 (mm-30) cc_final: 0.3232 (mp0) REVERT: A 482 ARG cc_start: 0.7411 (mtm180) cc_final: 0.7103 (mtp85) REVERT: A 557 MET cc_start: 0.5582 (ttp) cc_final: 0.5150 (mpp) REVERT: D 81 ASN cc_start: 0.5601 (t0) cc_final: 0.4834 (t0) REVERT: D 195 LYS cc_start: 0.8996 (tttt) cc_final: 0.8441 (ttpt) REVERT: D 224 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7975 (mp0) REVERT: D 239 GLN cc_start: 0.7713 (tt0) cc_final: 0.7228 (tt0) REVERT: D 284 THR cc_start: 0.7640 (m) cc_final: 0.7267 (p) REVERT: D 365 TYR cc_start: 0.7664 (m-80) cc_final: 0.7289 (m-80) REVERT: D 368 LEU cc_start: 0.7968 (tp) cc_final: 0.7696 (tp) REVERT: D 387 LEU cc_start: 0.6770 (mt) cc_final: 0.6285 (mt) REVERT: D 398 ASP cc_start: 0.7670 (m-30) cc_final: 0.7276 (m-30) REVERT: D 405 ASP cc_start: 0.8041 (m-30) cc_final: 0.7260 (p0) REVERT: D 421 TYR cc_start: 0.6769 (m-80) cc_final: 0.6450 (m-80) REVERT: D 441 LEU cc_start: 0.6506 (mt) cc_final: 0.6023 (mp) REVERT: D 542 ASN cc_start: 0.8504 (t0) cc_final: 0.8070 (t0) REVERT: D 586 ASP cc_start: 0.7219 (t70) cc_final: 0.6903 (t0) REVERT: D 856 ASN cc_start: 0.7314 (m-40) cc_final: 0.7057 (m-40) REVERT: D 979 ASP cc_start: 0.8417 (m-30) cc_final: 0.8178 (m-30) REVERT: D 1114 ILE cc_start: 0.8889 (mm) cc_final: 0.8619 (mm) outliers start: 1 outliers final: 1 residues processed: 763 average time/residue: 0.4312 time to fit residues: 509.6013 Evaluate side-chains 374 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 373 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 391 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 0.0060 chunk 285 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 179 optimal weight: 0.5980 chunk 219 optimal weight: 9.9990 chunk 342 optimal weight: 3.9990 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 317 ASN B 360 ASN B 394 ASN B 474 GLN B 556 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 99 ASN C 148 ASN C 334 ASN C 437 ASN C 703 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 914 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 81 GLN A 103 ASN A 121 ASN A 429 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS D 99 ASN D 134 GLN D 173 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 641 ASN D 787 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30444 Z= 0.311 Angle : 0.635 8.325 41396 Z= 0.334 Chirality : 0.047 0.200 4616 Planarity : 0.004 0.046 5375 Dihedral : 4.470 45.949 4051 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.39 % Allowed : 10.36 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -1.74 (0.12), residues: 3733 helix: -0.41 (0.15), residues: 1043 sheet: -1.28 (0.17), residues: 736 loop : -1.49 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 203 HIS 0.010 0.001 HIS A 195 PHE 0.022 0.002 PHE B 541 TYR 0.024 0.002 TYR A 381 ARG 0.006 0.001 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 458 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.6334 (p0) cc_final: 0.5597 (t70) REVERT: B 102 ARG cc_start: 0.6765 (mmm-85) cc_final: 0.6228 (mtp-110) REVERT: B 104 TRP cc_start: 0.7852 (m-90) cc_final: 0.7264 (m-90) REVERT: B 106 PHE cc_start: 0.7370 (m-80) cc_final: 0.6027 (m-80) REVERT: B 140 PHE cc_start: 0.6553 (p90) cc_final: 0.6151 (p90) REVERT: B 168 PHE cc_start: 0.6894 (t80) cc_final: 0.6674 (t80) REVERT: B 191 GLU cc_start: 0.8114 (tt0) cc_final: 0.7720 (tp30) REVERT: B 402 ILE cc_start: 0.5750 (pt) cc_final: 0.5237 (pt) REVERT: B 456 PHE cc_start: 0.6631 (m-80) cc_final: 0.6364 (m-80) REVERT: C 102 ARG cc_start: 0.7186 (mmt90) cc_final: 0.6599 (tpp80) REVERT: C 129 LYS cc_start: 0.7779 (mttt) cc_final: 0.7562 (ttmm) REVERT: C 191 GLU cc_start: 0.5879 (tt0) cc_final: 0.5381 (tt0) REVERT: C 202 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7536 (mtmt) REVERT: C 242 LEU cc_start: 0.7234 (mt) cc_final: 0.6983 (mt) REVERT: C 584 ILE cc_start: 0.8349 (mt) cc_final: 0.7878 (mt) REVERT: C 585 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8101 (pp) REVERT: C 603 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.7850 (t0) REVERT: C 973 ILE cc_start: 0.9254 (mm) cc_final: 0.8975 (mt) REVERT: A 35 GLU cc_start: 0.7942 (mt-10) cc_final: 0.6727 (tp30) REVERT: A 312 GLU cc_start: 0.4263 (OUTLIER) cc_final: 0.3965 (mm-30) REVERT: A 322 ASN cc_start: 0.5180 (p0) cc_final: 0.4849 (t0) REVERT: A 323 MET cc_start: 0.3010 (mmt) cc_final: 0.2698 (mtt) REVERT: A 376 MET cc_start: 0.3482 (mtt) cc_final: 0.2675 (mpp) REVERT: A 482 ARG cc_start: 0.7730 (mtm180) cc_final: 0.7249 (mtp85) REVERT: A 504 PHE cc_start: 0.3882 (OUTLIER) cc_final: 0.3438 (t80) REVERT: A 601 ASN cc_start: 0.4637 (t0) cc_final: 0.4414 (t0) REVERT: D 92 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.8016 (t80) REVERT: D 284 THR cc_start: 0.7737 (m) cc_final: 0.7324 (p) REVERT: D 365 TYR cc_start: 0.7886 (m-80) cc_final: 0.7601 (m-80) REVERT: D 387 LEU cc_start: 0.7159 (mt) cc_final: 0.6871 (mt) REVERT: D 398 ASP cc_start: 0.8134 (m-30) cc_final: 0.7611 (m-30) REVERT: D 516 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6667 (mp0) REVERT: D 544 ASN cc_start: 0.8033 (p0) cc_final: 0.6808 (t0) REVERT: D 574 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7678 (t70) REVERT: D 586 ASP cc_start: 0.6998 (t70) cc_final: 0.6744 (t0) REVERT: D 751 ASN cc_start: 0.8661 (m-40) cc_final: 0.8354 (m110) REVERT: D 856 ASN cc_start: 0.7412 (m-40) cc_final: 0.7159 (m-40) REVERT: D 985 ASP cc_start: 0.8226 (p0) cc_final: 0.7945 (p0) REVERT: D 1114 ILE cc_start: 0.9002 (mm) cc_final: 0.8736 (mm) outliers start: 79 outliers final: 51 residues processed: 518 average time/residue: 0.3825 time to fit residues: 323.0395 Evaluate side-chains 382 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 324 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 574 ASP Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 1074 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 284 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 1.9990 chunk 370 optimal weight: 1.9990 chunk 305 optimal weight: 6.9990 chunk 340 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 755 GLN B 804 GLN B 901 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C 965 GLN A 34 HIS A 49 ASN A 58 ASN A 139 GLN A 417 HIS A 522 GLN D 115 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN D 655 HIS D 774 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 30444 Z= 0.285 Angle : 0.596 11.296 41396 Z= 0.309 Chirality : 0.045 0.204 4616 Planarity : 0.004 0.047 5375 Dihedral : 4.457 40.069 4051 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.45 % Allowed : 12.63 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -1.17 (0.13), residues: 3733 helix: 0.36 (0.16), residues: 1029 sheet: -0.89 (0.18), residues: 731 loop : -1.34 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 48 HIS 0.005 0.001 HIS D 655 PHE 0.021 0.002 PHE D 643 TYR 0.020 0.002 TYR A 510 ARG 0.010 0.001 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 354 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.6355 (p0) cc_final: 0.5551 (t0) REVERT: B 168 PHE cc_start: 0.6737 (t80) cc_final: 0.6179 (t80) REVERT: B 191 GLU cc_start: 0.8123 (tt0) cc_final: 0.7764 (tp30) REVERT: B 200 TYR cc_start: 0.7458 (m-80) cc_final: 0.7253 (m-80) REVERT: B 241 LEU cc_start: 0.8042 (mt) cc_final: 0.7718 (mp) REVERT: B 402 ILE cc_start: 0.6311 (pt) cc_final: 0.6017 (pt) REVERT: B 456 PHE cc_start: 0.6563 (m-80) cc_final: 0.6231 (m-80) REVERT: B 552 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6496 (tp) REVERT: B 965 GLN cc_start: 0.7533 (mt0) cc_final: 0.7238 (mt0) REVERT: C 92 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6935 (t80) REVERT: C 129 LYS cc_start: 0.7870 (mttt) cc_final: 0.7535 (ttmm) REVERT: C 191 GLU cc_start: 0.6026 (tt0) cc_final: 0.4889 (tt0) REVERT: C 584 ILE cc_start: 0.8399 (mt) cc_final: 0.7929 (mt) REVERT: C 585 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7905 (pp) REVERT: C 904 TYR cc_start: 0.7132 (t80) cc_final: 0.6396 (t80) REVERT: A 35 GLU cc_start: 0.8094 (mt-10) cc_final: 0.6785 (tp30) REVERT: A 323 MET cc_start: 0.2691 (mmt) cc_final: 0.2201 (mtt) REVERT: A 376 MET cc_start: 0.3541 (mtt) cc_final: 0.2708 (mpp) REVERT: A 482 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7259 (mtp85) REVERT: A 610 TRP cc_start: 0.3231 (t-100) cc_final: 0.2749 (t-100) REVERT: D 56 LEU cc_start: 0.9098 (tp) cc_final: 0.8758 (tt) REVERT: D 284 THR cc_start: 0.7758 (m) cc_final: 0.7339 (p) REVERT: D 398 ASP cc_start: 0.8166 (m-30) cc_final: 0.7668 (m-30) REVERT: D 516 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6935 (mp0) REVERT: D 524 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7145 (t) REVERT: D 544 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7158 (t0) REVERT: D 574 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7613 (t70) REVERT: D 586 ASP cc_start: 0.6995 (t70) cc_final: 0.6764 (t0) REVERT: D 751 ASN cc_start: 0.8772 (m-40) cc_final: 0.8544 (m110) REVERT: D 856 ASN cc_start: 0.7301 (m-40) cc_final: 0.7029 (m-40) REVERT: D 979 ASP cc_start: 0.8664 (m-30) cc_final: 0.7491 (t0) REVERT: D 985 ASP cc_start: 0.8109 (p0) cc_final: 0.7361 (m-30) REVERT: D 1114 ILE cc_start: 0.9107 (mm) cc_final: 0.8746 (mm) outliers start: 114 outliers final: 81 residues processed: 439 average time/residue: 0.4004 time to fit residues: 290.0299 Evaluate side-chains 389 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 302 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 574 ASP Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain D residue 1119 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 0.9990 chunk 257 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 344 optimal weight: 0.7980 chunk 364 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 326 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 556 ASN B 655 HIS B 703 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 926 GLN C 969 ASN A 49 ASN A 290 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS D 370 ASN D 641 ASN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30444 Z= 0.171 Angle : 0.509 9.237 41396 Z= 0.263 Chirality : 0.043 0.222 4616 Planarity : 0.004 0.064 5375 Dihedral : 4.080 20.661 4050 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.60 % Allowed : 15.11 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.69 (0.13), residues: 3733 helix: 0.86 (0.17), residues: 1029 sheet: -0.60 (0.18), residues: 742 loop : -1.11 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 258 HIS 0.004 0.001 HIS A 401 PHE 0.023 0.001 PHE B 377 TYR 0.018 0.001 TYR B 495 ARG 0.007 0.001 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 358 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.6297 (p0) cc_final: 0.5681 (t70) REVERT: B 168 PHE cc_start: 0.6710 (t80) cc_final: 0.6216 (t80) REVERT: B 241 LEU cc_start: 0.8017 (mt) cc_final: 0.7662 (mp) REVERT: B 402 ILE cc_start: 0.6520 (pt) cc_final: 0.6131 (pt) REVERT: B 456 PHE cc_start: 0.6652 (m-80) cc_final: 0.6272 (m-80) REVERT: C 129 LYS cc_start: 0.7639 (mttt) cc_final: 0.7312 (ttmm) REVERT: C 191 GLU cc_start: 0.5828 (tt0) cc_final: 0.5396 (mt-10) REVERT: C 584 ILE cc_start: 0.8326 (mt) cc_final: 0.7855 (mt) REVERT: C 585 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7955 (pp) REVERT: C 703 ASN cc_start: 0.8250 (t0) cc_final: 0.7812 (t0) REVERT: C 881 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9127 (t) REVERT: C 904 TYR cc_start: 0.7037 (t80) cc_final: 0.6305 (t80) REVERT: C 926 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: A 35 GLU cc_start: 0.8106 (mt-10) cc_final: 0.6784 (tp30) REVERT: A 82 MET cc_start: 0.6177 (mtt) cc_final: 0.5800 (mtm) REVERT: A 323 MET cc_start: 0.2926 (mmt) cc_final: 0.2282 (mtt) REVERT: A 376 MET cc_start: 0.3488 (mtt) cc_final: 0.2728 (mpp) REVERT: A 401 HIS cc_start: 0.3304 (t-90) cc_final: 0.3089 (t-90) REVERT: A 482 ARG cc_start: 0.7910 (mtm180) cc_final: 0.7370 (mtp85) REVERT: D 56 LEU cc_start: 0.9089 (tp) cc_final: 0.8798 (tt) REVERT: D 284 THR cc_start: 0.7817 (m) cc_final: 0.7462 (p) REVERT: D 317 ASN cc_start: 0.8267 (m-40) cc_final: 0.8039 (m-40) REVERT: D 398 ASP cc_start: 0.8247 (m-30) cc_final: 0.7709 (m-30) REVERT: D 516 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6751 (mp0) REVERT: D 524 VAL cc_start: 0.7661 (OUTLIER) cc_final: 0.7053 (t) REVERT: D 544 ASN cc_start: 0.7894 (p0) cc_final: 0.7269 (t0) REVERT: D 751 ASN cc_start: 0.8746 (m-40) cc_final: 0.8514 (m110) REVERT: D 856 ASN cc_start: 0.7262 (m-40) cc_final: 0.6994 (m-40) REVERT: D 979 ASP cc_start: 0.8615 (m-30) cc_final: 0.7623 (t0) REVERT: D 1114 ILE cc_start: 0.9092 (mm) cc_final: 0.8702 (mm) outliers start: 86 outliers final: 58 residues processed: 421 average time/residue: 0.3826 time to fit residues: 266.4893 Evaluate side-chains 373 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 311 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1051 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 251 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 327 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 613 GLN B 703 ASN B 804 GLN B 935 GLN B 960 ASN B1005 GLN B1010 GLN C 66 HIS ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN ** D 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 30444 Z= 0.590 Angle : 0.841 14.111 41396 Z= 0.443 Chirality : 0.053 0.285 4616 Planarity : 0.006 0.065 5375 Dihedral : 5.879 25.855 4050 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.97 % Allowed : 15.48 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -1.46 (0.13), residues: 3733 helix: -0.01 (0.16), residues: 1024 sheet: -0.75 (0.19), residues: 700 loop : -1.58 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 258 HIS 0.008 0.002 HIS A 373 PHE 0.027 0.003 PHE C 275 TYR 0.039 0.003 TYR C 91 ARG 0.011 0.001 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 335 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 PHE cc_start: 0.7325 (t80) cc_final: 0.6816 (t80) REVERT: B 87 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7794 (p0) REVERT: B 88 ASP cc_start: 0.6712 (p0) cc_final: 0.6102 (t70) REVERT: B 140 PHE cc_start: 0.5638 (p90) cc_final: 0.5424 (p90) REVERT: B 241 LEU cc_start: 0.8045 (mt) cc_final: 0.7614 (mt) REVERT: B 377 PHE cc_start: 0.5620 (t80) cc_final: 0.5345 (t80) REVERT: B 402 ILE cc_start: 0.6122 (pt) cc_final: 0.5896 (pt) REVERT: B 456 PHE cc_start: 0.6471 (m-80) cc_final: 0.6258 (m-80) REVERT: C 572 THR cc_start: 0.8829 (m) cc_final: 0.8596 (p) REVERT: C 584 ILE cc_start: 0.8496 (mt) cc_final: 0.8047 (mt) REVERT: C 703 ASN cc_start: 0.8180 (t0) cc_final: 0.7601 (t0) REVERT: C 904 TYR cc_start: 0.7489 (t80) cc_final: 0.7165 (t80) REVERT: A 82 MET cc_start: 0.6078 (mtt) cc_final: 0.5805 (mtm) REVERT: A 297 MET cc_start: 0.2934 (ptp) cc_final: 0.2538 (ptp) REVERT: A 323 MET cc_start: 0.3356 (mmt) cc_final: 0.2494 (mtt) REVERT: A 369 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.5935 (t80) REVERT: A 376 MET cc_start: 0.3942 (mtt) cc_final: 0.3120 (mtp) REVERT: A 482 ARG cc_start: 0.8051 (mtm180) cc_final: 0.7505 (mtp85) REVERT: A 610 TRP cc_start: 0.2976 (t-100) cc_final: 0.2588 (t-100) REVERT: D 56 LEU cc_start: 0.9231 (tp) cc_final: 0.9022 (tt) REVERT: D 233 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8284 (mp) REVERT: D 473 TYR cc_start: 0.3926 (t80) cc_final: 0.3493 (t80) REVERT: D 524 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7229 (t) REVERT: D 544 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7908 (t0) REVERT: D 858 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8616 (mt) REVERT: D 979 ASP cc_start: 0.8746 (m-30) cc_final: 0.7601 (t0) REVERT: D 985 ASP cc_start: 0.8463 (p0) cc_final: 0.8149 (p0) outliers start: 164 outliers final: 114 residues processed: 464 average time/residue: 0.3900 time to fit residues: 300.8431 Evaluate side-chains 408 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 288 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 486 PHE Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 883 THR Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1021 SER Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 0.9990 chunk 328 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 364 optimal weight: 0.8980 chunk 302 optimal weight: 8.9990 chunk 168 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 913 GLN A 64 ASN A 96 GLN A 401 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN D 173 GLN D 641 ASN D 762 GLN D 774 GLN D 957 GLN D 992 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30444 Z= 0.170 Angle : 0.559 14.284 41396 Z= 0.290 Chirality : 0.044 0.184 4616 Planarity : 0.004 0.086 5375 Dihedral : 4.706 31.811 4050 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.39 % Allowed : 17.87 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.13), residues: 3733 helix: 0.83 (0.17), residues: 1009 sheet: -0.58 (0.19), residues: 702 loop : -1.19 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 353 HIS 0.004 0.001 HIS A 535 PHE 0.022 0.001 PHE C 823 TYR 0.031 0.001 TYR C 351 ARG 0.010 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 341 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.6599 (p0) cc_final: 0.6121 (t70) REVERT: B 117 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.6068 (tt) REVERT: B 153 MET cc_start: -0.0309 (OUTLIER) cc_final: -0.0797 (tmm) REVERT: B 168 PHE cc_start: 0.7092 (t80) cc_final: 0.6729 (t80) REVERT: B 227 VAL cc_start: 0.8585 (p) cc_final: 0.8360 (t) REVERT: B 241 LEU cc_start: 0.8158 (mt) cc_final: 0.7760 (mt) REVERT: B 269 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.6300 (p90) REVERT: B 402 ILE cc_start: 0.6542 (pt) cc_final: 0.6234 (pt) REVERT: B 456 PHE cc_start: 0.6552 (m-80) cc_final: 0.6329 (m-10) REVERT: C 191 GLU cc_start: 0.7406 (tt0) cc_final: 0.6656 (tp30) REVERT: C 324 GLU cc_start: 0.7430 (mp0) cc_final: 0.7121 (pm20) REVERT: C 336 CYS cc_start: 0.2441 (OUTLIER) cc_final: 0.1122 (t) REVERT: C 584 ILE cc_start: 0.8302 (mt) cc_final: 0.7745 (mt) REVERT: C 703 ASN cc_start: 0.8279 (t0) cc_final: 0.7743 (t0) REVERT: C 904 TYR cc_start: 0.7184 (t80) cc_final: 0.6768 (t80) REVERT: A 323 MET cc_start: 0.3035 (mmt) cc_final: 0.1654 (mtt) REVERT: A 325 GLN cc_start: 0.6936 (tm-30) cc_final: 0.5579 (pt0) REVERT: A 360 MET cc_start: 0.3449 (mtt) cc_final: 0.3091 (mtt) REVERT: A 376 MET cc_start: 0.3645 (mtt) cc_final: 0.2983 (mmm) REVERT: A 482 ARG cc_start: 0.7920 (mtm180) cc_final: 0.7386 (mtt-85) REVERT: D 56 LEU cc_start: 0.9172 (tp) cc_final: 0.8924 (tt) REVERT: D 233 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8450 (mp) REVERT: D 317 ASN cc_start: 0.8374 (m-40) cc_final: 0.8157 (m-40) REVERT: D 398 ASP cc_start: 0.8096 (m-30) cc_final: 0.7380 (m-30) REVERT: D 402 ILE cc_start: 0.6192 (pt) cc_final: 0.5973 (mt) REVERT: D 495 TYR cc_start: 0.5156 (m-80) cc_final: 0.4351 (m-80) REVERT: D 524 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7437 (t) REVERT: D 544 ASN cc_start: 0.7912 (p0) cc_final: 0.7654 (t0) REVERT: D 751 ASN cc_start: 0.8815 (m-40) cc_final: 0.8614 (m110) REVERT: D 979 ASP cc_start: 0.8575 (m-30) cc_final: 0.7833 (t0) REVERT: D 985 ASP cc_start: 0.8383 (p0) cc_final: 0.8018 (p0) outliers start: 112 outliers final: 72 residues processed: 427 average time/residue: 0.3778 time to fit residues: 267.6220 Evaluate side-chains 382 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 304 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 1021 SER Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 307 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 363 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 703 ASN B1005 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 641 ASN D 957 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30444 Z= 0.287 Angle : 0.603 13.507 41396 Z= 0.313 Chirality : 0.045 0.207 4616 Planarity : 0.004 0.076 5375 Dihedral : 4.855 28.160 4050 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.60 % Allowed : 17.99 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -0.78 (0.13), residues: 3733 helix: 0.73 (0.16), residues: 1021 sheet: -0.53 (0.19), residues: 717 loop : -1.17 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 48 HIS 0.007 0.001 HIS D 245 PHE 0.025 0.002 PHE B 338 TYR 0.032 0.002 TYR C 351 ARG 0.007 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 318 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7654 (p0) REVERT: B 88 ASP cc_start: 0.6896 (p0) cc_final: 0.6538 (t70) REVERT: B 153 MET cc_start: -0.0565 (OUTLIER) cc_final: -0.1068 (tmm) REVERT: B 241 LEU cc_start: 0.8216 (mt) cc_final: 0.7827 (mt) REVERT: B 269 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6394 (p90) REVERT: B 402 ILE cc_start: 0.6319 (pt) cc_final: 0.6063 (pt) REVERT: B 456 PHE cc_start: 0.6335 (m-80) cc_final: 0.6130 (m-10) REVERT: B 1107 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6700 (tpt90) REVERT: C 191 GLU cc_start: 0.7922 (tt0) cc_final: 0.6944 (tp30) REVERT: C 452 ARG cc_start: 0.4716 (mtt180) cc_final: 0.4298 (mmt90) REVERT: C 581 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8616 (p) REVERT: C 584 ILE cc_start: 0.8439 (mt) cc_final: 0.7964 (mt) REVERT: C 703 ASN cc_start: 0.8265 (t0) cc_final: 0.7820 (t0) REVERT: C 904 TYR cc_start: 0.7317 (t80) cc_final: 0.6915 (t80) REVERT: C 1029 MET cc_start: 0.8458 (tpp) cc_final: 0.7965 (ttm) REVERT: A 35 GLU cc_start: 0.8167 (mt-10) cc_final: 0.6966 (tp30) REVERT: A 82 MET cc_start: 0.6178 (mtt) cc_final: 0.5599 (mtm) REVERT: A 323 MET cc_start: 0.3241 (mmt) cc_final: 0.1920 (mtt) REVERT: A 360 MET cc_start: 0.3258 (mtt) cc_final: 0.2955 (mtt) REVERT: A 376 MET cc_start: 0.3847 (mtt) cc_final: 0.3078 (mtp) REVERT: A 478 TRP cc_start: 0.7086 (OUTLIER) cc_final: 0.5506 (t60) REVERT: A 482 ARG cc_start: 0.7960 (mtm180) cc_final: 0.7221 (mtp85) REVERT: A 610 TRP cc_start: 0.3084 (t-100) cc_final: 0.2560 (t-100) REVERT: D 56 LEU cc_start: 0.9168 (tp) cc_final: 0.8953 (tt) REVERT: D 233 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8272 (mp) REVERT: D 402 ILE cc_start: 0.6261 (pt) cc_final: 0.6049 (mt) REVERT: D 495 TYR cc_start: 0.5214 (m-80) cc_final: 0.4513 (m-80) REVERT: D 524 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7309 (t) REVERT: D 544 ASN cc_start: 0.8040 (p0) cc_final: 0.7586 (t0) REVERT: D 553 THR cc_start: 0.8448 (t) cc_final: 0.8010 (p) REVERT: D 751 ASN cc_start: 0.8811 (m-40) cc_final: 0.8605 (m110) REVERT: D 979 ASP cc_start: 0.8593 (m-30) cc_final: 0.7838 (t0) REVERT: D 985 ASP cc_start: 0.8403 (p0) cc_final: 0.8016 (p0) outliers start: 119 outliers final: 90 residues processed: 409 average time/residue: 0.3803 time to fit residues: 257.8315 Evaluate side-chains 392 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 295 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 478 TRP Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 1021 SER Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 0.3980 chunk 145 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 231 optimal weight: 0.0030 chunk 247 optimal weight: 20.0000 chunk 179 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 285 optimal weight: 4.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN D 409 GLN D 641 ASN D 957 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30444 Z= 0.215 Angle : 0.556 13.643 41396 Z= 0.287 Chirality : 0.044 0.231 4616 Planarity : 0.004 0.072 5375 Dihedral : 4.604 28.215 4050 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.51 % Allowed : 18.53 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: 3733 helix: 0.96 (0.17), residues: 1012 sheet: -0.48 (0.19), residues: 704 loop : -1.12 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 48 HIS 0.004 0.001 HIS D 245 PHE 0.021 0.001 PHE B 377 TYR 0.025 0.001 TYR C 351 ARG 0.007 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 318 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.6854 (p0) cc_final: 0.6462 (t70) REVERT: B 153 MET cc_start: -0.0414 (OUTLIER) cc_final: -0.0894 (tmm) REVERT: B 168 PHE cc_start: 0.7247 (t80) cc_final: 0.6935 (t80) REVERT: B 269 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.6302 (p90) REVERT: B 338 PHE cc_start: 0.6602 (m-10) cc_final: 0.5447 (p90) REVERT: B 402 ILE cc_start: 0.6478 (pt) cc_final: 0.6222 (pt) REVERT: B 1107 ARG cc_start: 0.7286 (mtt180) cc_final: 0.6705 (tpt90) REVERT: C 191 GLU cc_start: 0.8012 (tt0) cc_final: 0.7050 (tp30) REVERT: C 324 GLU cc_start: 0.7417 (mp0) cc_final: 0.6969 (pm20) REVERT: C 452 ARG cc_start: 0.4952 (mtt180) cc_final: 0.4685 (mmm-85) REVERT: C 581 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8572 (p) REVERT: C 584 ILE cc_start: 0.8392 (mt) cc_final: 0.7880 (mt) REVERT: C 703 ASN cc_start: 0.8288 (t0) cc_final: 0.7842 (t0) REVERT: C 904 TYR cc_start: 0.7250 (t80) cc_final: 0.6845 (t80) REVERT: C 985 ASP cc_start: 0.7431 (p0) cc_final: 0.6976 (p0) REVERT: A 35 GLU cc_start: 0.8119 (mt-10) cc_final: 0.6917 (tp30) REVERT: A 82 MET cc_start: 0.6691 (mtt) cc_final: 0.6435 (mtm) REVERT: A 323 MET cc_start: 0.2990 (mmt) cc_final: 0.1661 (mtt) REVERT: A 325 GLN cc_start: 0.7009 (tm-30) cc_final: 0.5709 (pt0) REVERT: A 360 MET cc_start: 0.3458 (mtt) cc_final: 0.3186 (mtt) REVERT: A 376 MET cc_start: 0.3783 (mtt) cc_final: 0.2989 (mtp) REVERT: A 478 TRP cc_start: 0.7106 (OUTLIER) cc_final: 0.5196 (t60) REVERT: A 482 ARG cc_start: 0.7918 (mtm180) cc_final: 0.7188 (mtt-85) REVERT: A 557 MET cc_start: 0.7901 (mpp) cc_final: 0.5609 (ttp) REVERT: D 56 LEU cc_start: 0.9157 (tp) cc_final: 0.8937 (tt) REVERT: D 233 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8267 (mp) REVERT: D 398 ASP cc_start: 0.8262 (m-30) cc_final: 0.7818 (m-30) REVERT: D 495 TYR cc_start: 0.5280 (m-80) cc_final: 0.4575 (m-80) REVERT: D 524 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7429 (t) REVERT: D 544 ASN cc_start: 0.7939 (p0) cc_final: 0.7485 (t0) REVERT: D 979 ASP cc_start: 0.8523 (m-30) cc_final: 0.8026 (t0) REVERT: D 985 ASP cc_start: 0.8361 (p0) cc_final: 0.7994 (p0) outliers start: 116 outliers final: 89 residues processed: 409 average time/residue: 0.3795 time to fit residues: 257.8494 Evaluate side-chains 394 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 299 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 478 TRP Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 1021 SER Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 3.9990 chunk 348 optimal weight: 2.9990 chunk 317 optimal weight: 4.9990 chunk 338 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 320 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1005 GLN C 14 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 913 GLN C 969 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 ASN D 641 ASN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 30444 Z= 0.396 Angle : 0.687 13.101 41396 Z= 0.357 Chirality : 0.047 0.299 4616 Planarity : 0.005 0.072 5375 Dihedral : 5.263 29.584 4050 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.15 % Allowed : 18.59 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % 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: -1.01 (0.13), residues: 3733 helix: 0.50 (0.16), residues: 1028 sheet: -0.50 (0.20), residues: 695 loop : -1.36 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 48 HIS 0.006 0.001 HIS A 373 PHE 0.023 0.002 PHE C 392 TYR 0.037 0.002 TYR B 707 ARG 0.008 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 295 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.6622 (p0) cc_final: 0.6362 (t70) REVERT: B 140 PHE cc_start: 0.5011 (p90) cc_final: 0.4771 (p90) REVERT: B 153 MET cc_start: -0.0438 (OUTLIER) cc_final: -0.0857 (tmm) REVERT: B 241 LEU cc_start: 0.7672 (mm) cc_final: 0.7075 (mt) REVERT: B 269 TYR cc_start: 0.6726 (OUTLIER) cc_final: 0.6226 (p90) REVERT: B 402 ILE cc_start: 0.6399 (pt) cc_final: 0.6162 (pt) REVERT: B 1107 ARG cc_start: 0.7396 (mtt180) cc_final: 0.6722 (tpt90) REVERT: C 452 ARG cc_start: 0.4962 (mtt180) cc_final: 0.4647 (mmm-85) REVERT: C 584 ILE cc_start: 0.8338 (mt) cc_final: 0.7780 (mt) REVERT: C 904 TYR cc_start: 0.7385 (t80) cc_final: 0.7074 (t80) REVERT: C 985 ASP cc_start: 0.7179 (p0) cc_final: 0.6176 (p0) REVERT: C 1029 MET cc_start: 0.8419 (tpp) cc_final: 0.7940 (ttm) REVERT: C 1041 ASP cc_start: 0.7645 (m-30) cc_final: 0.7165 (m-30) REVERT: A 35 GLU cc_start: 0.8180 (mt-10) cc_final: 0.6895 (tp30) REVERT: A 323 MET cc_start: 0.3395 (mmt) cc_final: 0.2244 (mtt) REVERT: A 360 MET cc_start: 0.3113 (mtt) cc_final: 0.2860 (mtt) REVERT: A 376 MET cc_start: 0.3924 (mtt) cc_final: 0.3083 (mtp) REVERT: A 478 TRP cc_start: 0.7151 (OUTLIER) cc_final: 0.5325 (t60) REVERT: A 482 ARG cc_start: 0.7913 (mtm180) cc_final: 0.7174 (mtt-85) REVERT: A 610 TRP cc_start: 0.3299 (t-100) cc_final: 0.2752 (t-100) REVERT: D 233 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8234 (mp) REVERT: D 273 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7834 (mmt90) REVERT: D 495 TYR cc_start: 0.5349 (m-80) cc_final: 0.4732 (m-80) REVERT: D 524 VAL cc_start: 0.7651 (OUTLIER) cc_final: 0.7291 (t) REVERT: D 544 ASN cc_start: 0.7968 (p0) cc_final: 0.7607 (t0) REVERT: D 979 ASP cc_start: 0.8561 (m-30) cc_final: 0.7998 (t0) REVERT: D 985 ASP cc_start: 0.8373 (p0) cc_final: 0.8003 (p0) outliers start: 137 outliers final: 112 residues processed: 402 average time/residue: 0.3828 time to fit residues: 255.2150 Evaluate side-chains 406 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 288 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 478 TRP Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 1021 SER Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 9.9990 chunk 358 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 375 optimal weight: 0.0470 chunk 345 optimal weight: 0.7980 chunk 299 optimal weight: 0.8980 chunk 31 optimal weight: 0.0040 chunk 231 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 overall best weight: 0.5490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 239 GLN B 317 ASN B 540 ASN B1005 GLN C 641 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN C1142 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.6734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 30444 Z= 0.159 Angle : 0.556 12.543 41396 Z= 0.286 Chirality : 0.043 0.224 4616 Planarity : 0.004 0.090 5375 Dihedral : 4.549 30.884 4050 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.15 % Allowed : 20.68 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.61 (0.14), residues: 3733 helix: 1.00 (0.17), residues: 1021 sheet: -0.41 (0.19), residues: 705 loop : -1.15 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 886 HIS 0.003 0.001 HIS A 374 PHE 0.020 0.001 PHE D 133 TYR 0.022 0.001 TYR C 351 ARG 0.005 0.000 ARG C 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 332 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 PHE cc_start: 0.7260 (t80) cc_final: 0.6981 (t80) REVERT: B 241 LEU cc_start: 0.7755 (mm) cc_final: 0.7206 (mt) REVERT: B 338 PHE cc_start: 0.6514 (m-10) cc_final: 0.5487 (p90) REVERT: B 402 ILE cc_start: 0.6484 (pt) cc_final: 0.6230 (pt) REVERT: B 456 PHE cc_start: 0.6260 (m-10) cc_final: 0.5880 (m-80) REVERT: B 1107 ARG cc_start: 0.7325 (mtt180) cc_final: 0.6657 (tpt90) REVERT: C 102 ARG cc_start: 0.7058 (mmt-90) cc_final: 0.6341 (tpp-160) REVERT: C 191 GLU cc_start: 0.8107 (tt0) cc_final: 0.7134 (tp30) REVERT: C 324 GLU cc_start: 0.7268 (mp0) cc_final: 0.6959 (pm20) REVERT: C 584 ILE cc_start: 0.8271 (mt) cc_final: 0.7708 (mt) REVERT: C 585 LEU cc_start: 0.8066 (pp) cc_final: 0.7818 (pp) REVERT: C 703 ASN cc_start: 0.8311 (t0) cc_final: 0.7903 (t0) REVERT: C 708 SER cc_start: 0.8202 (p) cc_final: 0.7556 (m) REVERT: C 904 TYR cc_start: 0.7223 (t80) cc_final: 0.6799 (t80) REVERT: A 35 GLU cc_start: 0.8087 (mt-10) cc_final: 0.6854 (tp30) REVERT: A 325 GLN cc_start: 0.7046 (tm-30) cc_final: 0.5833 (pt0) REVERT: A 360 MET cc_start: 0.3482 (mtt) cc_final: 0.3253 (mtt) REVERT: A 376 MET cc_start: 0.3640 (mtt) cc_final: 0.3312 (mmm) REVERT: A 478 TRP cc_start: 0.7120 (OUTLIER) cc_final: 0.5254 (t60) REVERT: A 482 ARG cc_start: 0.7843 (mtm180) cc_final: 0.7167 (mtt-85) REVERT: A 557 MET cc_start: 0.7817 (mpp) cc_final: 0.5731 (ttp) REVERT: D 133 PHE cc_start: 0.7020 (m-80) cc_final: 0.6802 (m-80) REVERT: D 233 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8473 (mp) REVERT: D 291 CYS cc_start: 0.6726 (m) cc_final: 0.6518 (m) REVERT: D 398 ASP cc_start: 0.8296 (m-30) cc_final: 0.7938 (m-30) REVERT: D 452 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7751 (mtt-85) REVERT: D 495 TYR cc_start: 0.5434 (m-80) cc_final: 0.4477 (m-80) REVERT: D 544 ASN cc_start: 0.7717 (p0) cc_final: 0.7421 (t0) REVERT: D 586 ASP cc_start: 0.7856 (p0) cc_final: 0.7555 (p0) REVERT: D 979 ASP cc_start: 0.8465 (m-30) cc_final: 0.8086 (t0) REVERT: D 985 ASP cc_start: 0.8272 (p0) cc_final: 0.7965 (p0) outliers start: 71 outliers final: 56 residues processed: 391 average time/residue: 0.3908 time to fit residues: 251.7145 Evaluate side-chains 359 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 301 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 478 TRP Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 1021 SER Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain D residue 1119 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 6.9990 chunk 318 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 0.4980 chunk 299 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 307 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 239 GLN B 540 ASN B 544 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 955 ASN C 969 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 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 = 0.4321 r_free = 0.4321 target = 0.151015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.123943 restraints weight = 82881.925| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.82 r_work: 0.3769 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.6867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30444 Z= 0.251 Angle : 0.591 12.681 41396 Z= 0.305 Chirality : 0.045 0.301 4616 Planarity : 0.004 0.081 5375 Dihedral : 4.683 34.584 4050 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.33 % Allowed : 20.90 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.64 (0.14), residues: 3733 helix: 0.98 (0.17), residues: 1022 sheet: -0.48 (0.19), residues: 700 loop : -1.15 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 48 HIS 0.004 0.001 HIS A 378 PHE 0.026 0.002 PHE B 377 TYR 0.025 0.002 TYR B 707 ARG 0.006 0.000 ARG C 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7095.40 seconds wall clock time: 130 minutes 11.44 seconds (7811.44 seconds total)