Starting phenix.real_space_refine on Wed Feb 21 05:52:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w98_32361/02_2024/7w98_32361.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w98_32361/02_2024/7w98_32361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w98_32361/02_2024/7w98_32361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w98_32361/02_2024/7w98_32361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w98_32361/02_2024/7w98_32361.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w98_32361/02_2024/7w98_32361.pdb" } resolution = 3.6 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= 0.099 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 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 180": "OE1" <-> "OE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "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 TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ASP 427": "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 PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "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 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" 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 PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 30": "OD1" <-> "OD2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D ASP 206": "OD1" <-> "OD2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 299": "OD1" <-> "OD2" Residue "D ASP 303": "OD1" <-> "OD2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "D ASP 350": "OD1" <-> "OD2" Residue "D ASP 382": "OD1" <-> "OD2" Residue "D ASP 427": "OD1" <-> "OD2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 494": "OD1" <-> "OD2" Residue "D TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "D GLU 571": "OE1" <-> "OE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 597": "OD1" <-> "OD2" Residue "D ASP 609": "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 65": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "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 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "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 565": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "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 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C 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: "A" 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: "D" 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: "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 Time building chain proxies: 14.71, per 1000 atoms: 0.49 Number of scatterers: 29737 At special positions: 0 Unit cell: (157.392, 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.03 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 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: 11.01 Conformation dependent library (CDL) restraints added in 5.6 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: 93 helices and 50 sheets defined 30.1% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 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 364 through 369 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.956A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.721A 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 780 removed outlier: 3.598A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.835A 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 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.723A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.529A 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: 3.910A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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: 3.591A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.784A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.537A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.572A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.706A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.688A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.857A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.501A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 941 through 944 removed outlier: 3.644A pdb=" N ALA A 944 " --> pdb=" O THR A 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.704A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.828A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.194A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'D' and resid 21 through 53 removed outlier: 3.639A pdb=" N ALA D 25 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.533A pdb=" N SER D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.607A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.500A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.578A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.653A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 3.713A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.592A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.758A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.709A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.793A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 330 removed outlier: 3.742A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.569A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 397 through 414 removed outlier: 3.885A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D 404 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.520A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.161A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.722A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.893A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.733A pdb=" N THR D 593 " --> pdb=" O GLU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.221A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.999A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.691A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.718A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.649A 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: 3.520A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 772 " --> pdb=" O THR C 768 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.536A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.718A 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 887 through 891 removed outlier: 4.117A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.776A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.618A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.507A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 removed outlier: 3.784A pdb=" N ALA C 944 " --> pdb=" O THR C 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 941 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.694A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.527A 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: 4.459A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 4.307A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.761A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.548A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.623A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.711A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS B 537 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 552 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.777A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.689A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.464A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.912A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.186A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.529A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.627A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AC3, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.521A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.927A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.612A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.612A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.610A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.219A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.844A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.654A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.654A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.939A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 131 through 133 removed outlier: 3.925A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.282A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.899A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.587A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.767A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.836A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.393A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.861A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.635A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.617A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.149A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 721 removed outlier: 6.792A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 724 through 728 removed outlier: 3.664A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.885A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1145 hydrogen bonds defined for protein. 3174 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: 13.44 Time building geometry restraints manager: 12.06 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: 9633 1.35 - 1.47: 7572 1.47 - 1.59: 13045 1.59 - 1.71: 0 1.71 - 1.83: 194 Bond restraints: 30444 Sorted by residual: bond pdb=" N GLN A 14 " pdb=" CA GLN A 14 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.30e+00 bond pdb=" C SER A 383 " pdb=" N PRO A 384 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.18e+00 bond pdb=" N SER D 19 " pdb=" CA SER D 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+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 2.91e+00 bond pdb=" N GLN C 14 " pdb=" CA GLN C 14 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 30439 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.11: 705 106.11 - 113.09: 16156 113.09 - 120.07: 10343 120.07 - 127.05: 13855 127.05 - 134.03: 337 Bond angle restraints: 41396 Sorted by residual: angle pdb=" N ILE A 418 " pdb=" CA ILE A 418 " pdb=" C ILE A 418 " ideal model delta sigma weight residual 111.56 108.66 2.90 8.60e-01 1.35e+00 1.14e+01 angle pdb=" CA ILE C 664 " pdb=" C ILE C 664 " pdb=" N PRO C 665 " ideal model delta sigma weight residual 118.12 120.36 -2.24 8.10e-01 1.52e+00 7.64e+00 angle pdb=" CA ILE C 664 " pdb=" C ILE C 664 " pdb=" O ILE C 664 " ideal model delta sigma weight residual 120.88 119.02 1.86 6.80e-01 2.16e+00 7.46e+00 angle pdb=" N VAL D 581 " pdb=" CA VAL D 581 " pdb=" CB VAL D 581 " ideal model delta sigma weight residual 112.21 109.22 2.99 1.10e+00 8.26e-01 7.41e+00 angle pdb=" C GLU D 145 " pdb=" N PRO D 146 " pdb=" CA PRO D 146 " ideal model delta sigma weight residual 127.00 133.12 -6.12 2.40e+00 1.74e-01 6.49e+00 ... (remaining 41391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 16910 18.00 - 35.99: 996 35.99 - 53.99: 148 53.99 - 71.99: 53 71.99 - 89.98: 29 Dihedral angle restraints: 18136 sinusoidal: 7139 harmonic: 10997 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 47.46 45.54 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 52.92 40.08 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " pdb=" SG CYS D 542 " pdb=" CB CYS D 542 " ideal model delta sinusoidal sigma weight residual -86.00 -124.94 38.94 1 1.00e+01 1.00e-02 2.13e+01 ... (remaining 18133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3031 0.032 - 0.064: 1090 0.064 - 0.096: 227 0.096 - 0.128: 242 0.128 - 0.160: 26 Chirality restraints: 4616 Sorted by residual: chirality pdb=" CA ILE A 896 " pdb=" N ILE A 896 " pdb=" C ILE A 896 " pdb=" CB ILE A 896 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE B 896 " pdb=" N ILE B 896 " pdb=" C ILE B 896 " pdb=" CB ILE B 896 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 4613 not shown) Planarity restraints: 5375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 229 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO C 230 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 130 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C VAL C 130 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL C 130 " -0.010 2.00e-02 2.50e+03 pdb=" N CYS C 131 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 714 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO C 715 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 715 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 715 " 0.019 5.00e-02 4.00e+02 ... (remaining 5372 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 270 2.61 - 3.18: 25330 3.18 - 3.76: 44166 3.76 - 4.33: 63213 4.33 - 4.90: 104667 Nonbonded interactions: 237646 Sorted by model distance: nonbonded pdb=" OG1 THR A 883 " pdb=" OH TYR C 707 " model vdw 2.038 2.440 nonbonded pdb=" OE1 GLN B 965 " pdb=" OG SER B1003 " model vdw 2.078 2.440 nonbonded pdb=" O GLN A 755 " pdb=" OG SER C 968 " model vdw 2.100 2.440 nonbonded pdb=" O GLN B 755 " pdb=" OG SER A 968 " model vdw 2.105 2.440 nonbonded pdb=" OG SER B 711 " pdb=" OE1 GLN C 895 " model vdw 2.128 2.440 ... (remaining 237641 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 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 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: 0.020 Extract box with map and model: 11.000 Check model and map are aligned: 0.420 Set scattering table: 0.280 Process input model: 77.650 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.140 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 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 : 0.003 0.042 30444 Z= 0.224 Angle : 0.574 6.376 41396 Z= 0.321 Chirality : 0.041 0.160 4616 Planarity : 0.003 0.042 5375 Dihedral : 12.487 89.982 10934 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.03 % Allowed : 1.42 % Favored : 98.55 % 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: -3.30 (0.11), residues: 3733 helix: -2.22 (0.12), residues: 1002 sheet: -2.21 (0.17), residues: 665 loop : -2.17 (0.12), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 203 HIS 0.003 0.001 HIS C 49 PHE 0.011 0.001 PHE A 562 TYR 0.008 0.001 TYR B 873 ARG 0.003 0.000 ARG A 44 *********************** 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 762 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 761 time to evaluate : 3.176 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 117 LEU cc_start: 0.7976 (mp) cc_final: 0.7630 (tp) REVERT: B 129 LYS cc_start: 0.8317 (mttt) cc_final: 0.8101 (mtpp) REVERT: B 143 VAL cc_start: 0.6342 (t) cc_final: 0.5748 (t) REVERT: B 458 LYS cc_start: 0.5962 (mppt) cc_final: 0.5163 (pttm) REVERT: B 708 SER cc_start: 0.7260 (t) cc_final: 0.6813 (m) REVERT: B 752 LEU cc_start: 0.9290 (mp) cc_final: 0.8922 (tp) REVERT: B 756 TYR cc_start: 0.8576 (m-80) cc_final: 0.8091 (m-80) REVERT: B 859 THR cc_start: 0.7396 (m) cc_final: 0.7194 (t) REVERT: B 918 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7153 (mt-10) REVERT: B 1073 LYS cc_start: 0.8492 (mttt) cc_final: 0.8099 (mtpt) REVERT: A 58 PHE cc_start: 0.8306 (m-10) cc_final: 0.8052 (m-80) REVERT: A 119 ILE cc_start: 0.8698 (mt) cc_final: 0.8447 (mt) REVERT: A 216 LEU cc_start: 0.6490 (mt) cc_final: 0.6262 (mt) REVERT: A 298 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8261 (mt-10) REVERT: A 340 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7119 (pt0) REVERT: A 356 LYS cc_start: 0.5100 (ttmm) cc_final: 0.4501 (mmmm) REVERT: A 389 ASP cc_start: 0.6236 (m-30) cc_final: 0.5731 (m-30) REVERT: A 703 ASN cc_start: 0.7636 (m-40) cc_final: 0.7387 (t0) REVERT: A 751 ASN cc_start: 0.8820 (m-40) cc_final: 0.7961 (m-40) REVERT: A 752 LEU cc_start: 0.8921 (mt) cc_final: 0.8355 (mt) REVERT: A 973 ILE cc_start: 0.9343 (tt) cc_final: 0.9140 (tp) REVERT: A 979 ASP cc_start: 0.8558 (m-30) cc_final: 0.8271 (m-30) REVERT: A 984 LEU cc_start: 0.7725 (mp) cc_final: 0.6816 (mt) REVERT: D 32 PHE cc_start: 0.7028 (t80) cc_final: 0.6803 (t80) REVERT: D 323 MET cc_start: 0.4042 (mmt) cc_final: 0.3053 (mmt) REVERT: D 383 MET cc_start: 0.6514 (mtp) cc_final: 0.6309 (ppp) REVERT: D 557 MET cc_start: 0.3220 (ttp) cc_final: 0.2942 (ptm) REVERT: C 19 ARG cc_start: 0.6689 (ptp-170) cc_final: 0.6352 (tpm170) REVERT: C 55 PHE cc_start: 0.8153 (m-80) cc_final: 0.7415 (m-80) REVERT: C 86 PHE cc_start: 0.5868 (t80) cc_final: 0.5620 (t80) REVERT: C 104 TRP cc_start: 0.7976 (m-90) cc_final: 0.7300 (m100) REVERT: C 229 LEU cc_start: 0.8658 (mt) cc_final: 0.8446 (mt) REVERT: C 237 ARG cc_start: 0.6232 (mtm180) cc_final: 0.5734 (mpp80) REVERT: C 270 LEU cc_start: 0.8407 (mp) cc_final: 0.8149 (mp) REVERT: C 979 ASP cc_start: 0.8565 (m-30) cc_final: 0.8189 (m-30) REVERT: C 981 LEU cc_start: 0.8165 (tp) cc_final: 0.7952 (tp) REVERT: C 983 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7608 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 762 average time/residue: 0.4215 time to fit residues: 505.2916 Evaluate side-chains 375 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 1.9990 chunk 285 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 295 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 342 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 207 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 317 ASN B 460 ASN B 481 ASN B 613 GLN B 907 ASN B 949 GLN B 955 ASN B1011 GLN A 66 HIS A 137 ASN A 149 ASN A 165 ASN A 188 ASN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 710 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 949 GLN A1088 HIS D 134 ASN D 508 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 137 ASN C 450 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1002 GLN C1083 HIS C1113 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30444 Z= 0.307 Angle : 0.650 9.004 41396 Z= 0.340 Chirality : 0.047 0.212 4616 Planarity : 0.004 0.042 5375 Dihedral : 4.461 21.828 4050 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.60 % Allowed : 10.08 % Favored : 87.31 % 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: -1.59 (0.13), residues: 3733 helix: 0.04 (0.15), residues: 1002 sheet: -1.38 (0.18), residues: 674 loop : -1.50 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 349 HIS 0.007 0.001 HIS D 535 PHE 0.027 0.002 PHE B 55 TYR 0.022 0.002 TYR A 495 ARG 0.007 0.001 ARG B 319 *********************** 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 523 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 437 time to evaluate : 3.172 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 128 ILE cc_start: 0.9179 (mp) cc_final: 0.8924 (mp) REVERT: B 195 LYS cc_start: 0.7190 (pptt) cc_final: 0.6188 (pttt) REVERT: B 304 LYS cc_start: 0.9228 (mmmm) cc_final: 0.9023 (tttt) REVERT: B 535 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7577 (tppp) REVERT: B 752 LEU cc_start: 0.9328 (mp) cc_final: 0.9043 (tp) REVERT: B 756 TYR cc_start: 0.8863 (m-80) cc_final: 0.8500 (m-80) REVERT: B 870 ILE cc_start: 0.9181 (mm) cc_final: 0.8836 (mt) REVERT: B 900 MET cc_start: 0.8481 (mmt) cc_final: 0.7549 (mpp) REVERT: B 995 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8029 (mtm-85) REVERT: B 1030 SER cc_start: 0.9160 (m) cc_final: 0.8777 (t) REVERT: B 1114 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8638 (tp) REVERT: A 177 MET cc_start: 0.1042 (mmt) cc_final: 0.0242 (mmt) REVERT: A 228 ASP cc_start: 0.8333 (t0) cc_final: 0.8124 (t0) REVERT: A 265 TYR cc_start: 0.7466 (p90) cc_final: 0.6717 (p90) REVERT: A 552 LEU cc_start: 0.8815 (mm) cc_final: 0.8480 (mm) REVERT: A 907 ASN cc_start: 0.9146 (t0) cc_final: 0.8842 (t0) REVERT: A 973 ILE cc_start: 0.9331 (tt) cc_final: 0.9035 (tp) REVERT: A 979 ASP cc_start: 0.8652 (m-30) cc_final: 0.8314 (m-30) REVERT: A 981 LEU cc_start: 0.8837 (tp) cc_final: 0.8593 (tt) REVERT: A 1041 ASP cc_start: 0.7436 (t0) cc_final: 0.7077 (t0) REVERT: A 1110 TYR cc_start: 0.8781 (t80) cc_final: 0.8475 (t80) REVERT: D 202 TYR cc_start: 0.6021 (t80) cc_final: 0.5682 (m-80) REVERT: D 323 MET cc_start: 0.4489 (mmt) cc_final: 0.2969 (mpp) REVERT: D 376 MET cc_start: 0.0948 (mtm) cc_final: 0.0603 (mtm) REVERT: D 557 MET cc_start: 0.3260 (ttp) cc_final: 0.2875 (ptm) REVERT: D 582 ARG cc_start: 0.6346 (mpt180) cc_final: 0.5624 (mmp-170) REVERT: C 19 ARG cc_start: 0.6708 (ptp-170) cc_final: 0.6195 (tpt170) REVERT: C 55 PHE cc_start: 0.8265 (m-80) cc_final: 0.7446 (m-80) REVERT: C 92 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7449 (t80) REVERT: C 104 TRP cc_start: 0.8117 (m-90) cc_final: 0.7791 (m100) REVERT: C 365 TYR cc_start: 0.8028 (m-80) cc_final: 0.7803 (m-80) REVERT: C 390 LEU cc_start: 0.7220 (mp) cc_final: 0.6447 (mt) REVERT: C 983 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7939 (ttm-80) REVERT: C 994 ASP cc_start: 0.8146 (t70) cc_final: 0.7773 (t0) outliers start: 86 outliers final: 54 residues processed: 495 average time/residue: 0.4104 time to fit residues: 329.1076 Evaluate side-chains 379 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 322 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 284 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 4.9990 chunk 370 optimal weight: 2.9990 chunk 305 optimal weight: 10.0000 chunk 340 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B1106 GLN A 343 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 710 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 764 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30444 Z= 0.318 Angle : 0.628 10.051 41396 Z= 0.329 Chirality : 0.046 0.223 4616 Planarity : 0.004 0.047 5375 Dihedral : 4.630 23.480 4050 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.15 % Allowed : 11.96 % Favored : 83.89 % 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: -1.10 (0.13), residues: 3733 helix: 0.70 (0.16), residues: 1008 sheet: -0.90 (0.19), residues: 683 loop : -1.43 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 64 HIS 0.007 0.001 HIS B 66 PHE 0.031 0.002 PHE B 65 TYR 0.018 0.002 TYR A 144 ARG 0.016 0.001 ARG A 246 *********************** 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 498 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 361 time to evaluate : 3.286 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 223 LEU cc_start: 0.8282 (mp) cc_final: 0.7875 (mt) REVERT: B 297 SER cc_start: 0.8763 (m) cc_final: 0.8350 (t) REVERT: B 408 ARG cc_start: 0.4088 (OUTLIER) cc_final: 0.3372 (tmm-80) REVERT: B 900 MET cc_start: 0.8616 (mmt) cc_final: 0.7662 (mpp) REVERT: B 918 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 957 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 1030 SER cc_start: 0.9029 (m) cc_final: 0.8775 (t) REVERT: B 1031 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 40 ASP cc_start: 0.8529 (t0) cc_final: 0.8312 (t0) REVERT: A 42 VAL cc_start: 0.9433 (OUTLIER) cc_final: 0.9028 (m) REVERT: A 110 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5990 (mm) REVERT: A 177 MET cc_start: -0.0448 (mmt) cc_final: -0.1044 (mmt) REVERT: A 200 TYR cc_start: 0.7478 (m-80) cc_final: 0.7144 (m-80) REVERT: A 338 PHE cc_start: 0.7603 (m-80) cc_final: 0.7018 (m-80) REVERT: A 368 LEU cc_start: 0.7831 (mp) cc_final: 0.7524 (mt) REVERT: A 552 LEU cc_start: 0.8861 (mm) cc_final: 0.8424 (mm) REVERT: A 703 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8288 (t0) REVERT: A 957 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 973 ILE cc_start: 0.9325 (tt) cc_final: 0.9069 (tp) REVERT: A 979 ASP cc_start: 0.8677 (m-30) cc_final: 0.8393 (m-30) REVERT: A 1017 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7763 (mm-30) REVERT: A 1041 ASP cc_start: 0.7490 (t0) cc_final: 0.7100 (t0) REVERT: A 1110 TYR cc_start: 0.8908 (t80) cc_final: 0.8565 (t80) REVERT: D 69 TRP cc_start: 0.6889 (t60) cc_final: 0.6686 (t60) REVERT: D 202 TYR cc_start: 0.6140 (t80) cc_final: 0.5794 (m-80) REVERT: D 323 MET cc_start: 0.3249 (mmt) cc_final: 0.3025 (mpp) REVERT: D 557 MET cc_start: 0.3210 (ttp) cc_final: 0.2856 (ptm) REVERT: D 579 MET cc_start: 0.1293 (mmt) cc_final: 0.0624 (mmm) REVERT: D 613 TYR cc_start: 0.2672 (p90) cc_final: 0.1869 (p90) REVERT: C 19 ARG cc_start: 0.6591 (ptp-170) cc_final: 0.5915 (tpt170) REVERT: C 55 PHE cc_start: 0.7957 (m-80) cc_final: 0.7033 (m-80) REVERT: C 92 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7536 (t80) REVERT: C 104 TRP cc_start: 0.8027 (m-90) cc_final: 0.7783 (m100) REVERT: C 177 MET cc_start: 0.2205 (tpp) cc_final: 0.1763 (ttp) REVERT: C 242 LEU cc_start: 0.7020 (mp) cc_final: 0.6652 (tt) REVERT: C 365 TYR cc_start: 0.7791 (m-80) cc_final: 0.7572 (m-80) REVERT: C 390 LEU cc_start: 0.7258 (mp) cc_final: 0.6513 (mt) REVERT: C 664 ILE cc_start: 0.8904 (mm) cc_final: 0.8530 (mm) REVERT: C 776 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8417 (ttpp) REVERT: C 994 ASP cc_start: 0.8290 (t70) cc_final: 0.7765 (t0) REVERT: C 1072 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7972 (mt-10) outliers start: 137 outliers final: 78 residues processed: 462 average time/residue: 0.3958 time to fit residues: 298.2973 Evaluate side-chains 387 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 303 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1121 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 0.6980 chunk 257 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 344 optimal weight: 0.9980 chunk 364 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 chunk 326 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN B 245 HIS A 137 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 955 ASN C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30444 Z= 0.166 Angle : 0.526 8.215 41396 Z= 0.272 Chirality : 0.043 0.179 4616 Planarity : 0.003 0.042 5375 Dihedral : 4.211 22.987 4050 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.82 % Allowed : 14.78 % Favored : 82.40 % 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: -0.64 (0.13), residues: 3733 helix: 1.21 (0.17), residues: 997 sheet: -0.62 (0.19), residues: 686 loop : -1.19 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 275 HIS 0.007 0.001 HIS D 540 PHE 0.020 0.001 PHE B 32 TYR 0.022 0.001 TYR B 144 ARG 0.006 0.000 ARG B 567 *********************** 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 476 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 383 time to evaluate : 3.464 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 128 ILE cc_start: 0.9196 (mp) cc_final: 0.8795 (pt) REVERT: B 223 LEU cc_start: 0.8057 (mp) cc_final: 0.7049 (mt) REVERT: B 297 SER cc_start: 0.8812 (m) cc_final: 0.8424 (p) REVERT: B 408 ARG cc_start: 0.4515 (OUTLIER) cc_final: 0.4048 (tmm-80) REVERT: B 567 ARG cc_start: 0.7268 (mtm-85) cc_final: 0.6986 (mtm-85) REVERT: B 698 SER cc_start: 0.8416 (t) cc_final: 0.8086 (p) REVERT: B 752 LEU cc_start: 0.9516 (tp) cc_final: 0.8974 (tp) REVERT: B 900 MET cc_start: 0.8535 (mmt) cc_final: 0.7758 (mpp) REVERT: B 957 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 177 MET cc_start: -0.1537 (mmt) cc_final: -0.1817 (mmt) REVERT: A 200 TYR cc_start: 0.7581 (m-80) cc_final: 0.7321 (m-80) REVERT: A 368 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7585 (mt) REVERT: A 552 LEU cc_start: 0.8827 (mm) cc_final: 0.8462 (mm) REVERT: A 787 GLN cc_start: 0.8008 (pm20) cc_final: 0.7695 (pm20) REVERT: A 925 ASN cc_start: 0.8389 (m-40) cc_final: 0.7989 (m-40) REVERT: A 957 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 1041 ASP cc_start: 0.7444 (t0) cc_final: 0.7018 (t0) REVERT: A 1110 TYR cc_start: 0.8887 (t80) cc_final: 0.8490 (t80) REVERT: D 192 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7770 (ttp80) REVERT: D 202 TYR cc_start: 0.6170 (t80) cc_final: 0.5804 (m-80) REVERT: D 239 HIS cc_start: 0.4025 (m-70) cc_final: 0.3767 (m170) REVERT: D 366 MET cc_start: 0.1092 (tpt) cc_final: 0.0882 (mtp) REVERT: D 408 MET cc_start: 0.5592 (tpp) cc_final: 0.5362 (tpt) REVERT: D 557 MET cc_start: 0.3308 (ttp) cc_final: 0.2899 (ptm) REVERT: D 573 VAL cc_start: 0.3619 (t) cc_final: 0.2905 (m) REVERT: D 587 TYR cc_start: 0.0542 (t80) cc_final: -0.0150 (t80) REVERT: C 19 ARG cc_start: 0.6335 (ptp-170) cc_final: 0.5899 (mmt180) REVERT: C 55 PHE cc_start: 0.8039 (m-80) cc_final: 0.7129 (m-80) REVERT: C 104 TRP cc_start: 0.8135 (m-90) cc_final: 0.7808 (m100) REVERT: C 177 MET cc_start: 0.2177 (tpp) cc_final: 0.1798 (ttp) REVERT: C 242 LEU cc_start: 0.7134 (mp) cc_final: 0.6761 (tt) REVERT: C 284 THR cc_start: 0.8623 (m) cc_final: 0.8143 (p) REVERT: C 365 TYR cc_start: 0.8127 (m-80) cc_final: 0.7888 (m-80) REVERT: C 568 ASP cc_start: 0.7740 (p0) cc_final: 0.7508 (p0) REVERT: C 664 ILE cc_start: 0.8823 (mm) cc_final: 0.8155 (mm) REVERT: C 994 ASP cc_start: 0.8102 (t70) cc_final: 0.7847 (t0) REVERT: C 1072 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7848 (mt-10) outliers start: 93 outliers final: 62 residues processed: 452 average time/residue: 0.3948 time to fit residues: 294.3643 Evaluate side-chains 385 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 320 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1121 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 310 optimal weight: 0.7980 chunk 251 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 245 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 165 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 787 GLN C 957 GLN C1106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30444 Z= 0.267 Angle : 0.583 7.933 41396 Z= 0.303 Chirality : 0.044 0.199 4616 Planarity : 0.004 0.041 5375 Dihedral : 4.499 25.188 4050 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.54 % Allowed : 15.69 % Favored : 80.77 % 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: -0.62 (0.13), residues: 3733 helix: 1.23 (0.17), residues: 1006 sheet: -0.53 (0.19), residues: 687 loop : -1.22 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 258 HIS 0.014 0.001 HIS B 245 PHE 0.020 0.002 PHE A 133 TYR 0.026 0.002 TYR D 237 ARG 0.005 0.001 ARG B 246 *********************** 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 449 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 332 time to evaluate : 3.676 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 128 ILE cc_start: 0.9246 (mp) cc_final: 0.8904 (pt) REVERT: B 223 LEU cc_start: 0.7949 (mp) cc_final: 0.7486 (mt) REVERT: B 297 SER cc_start: 0.8854 (m) cc_final: 0.8382 (t) REVERT: B 403 ARG cc_start: 0.4438 (mtm180) cc_final: 0.4170 (mtp85) REVERT: B 408 ARG cc_start: 0.4327 (OUTLIER) cc_final: 0.4109 (tmm-80) REVERT: B 458 LYS cc_start: 0.6554 (mptt) cc_final: 0.5725 (pttm) REVERT: B 900 MET cc_start: 0.8663 (mmt) cc_final: 0.8052 (mpp) REVERT: B 957 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7803 (tm-30) REVERT: A 177 MET cc_start: -0.1403 (mmt) cc_final: -0.1616 (mmt) REVERT: A 265 TYR cc_start: 0.7065 (p90) cc_final: 0.6815 (p90) REVERT: A 552 LEU cc_start: 0.8816 (mm) cc_final: 0.8407 (mm) REVERT: A 780 GLU cc_start: 0.8330 (tt0) cc_final: 0.8123 (tt0) REVERT: A 925 ASN cc_start: 0.8440 (m-40) cc_final: 0.8037 (m-40) REVERT: A 957 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 1110 TYR cc_start: 0.8906 (t80) cc_final: 0.8498 (t80) REVERT: D 323 MET cc_start: 0.3261 (mmt) cc_final: 0.2647 (mpp) REVERT: D 408 MET cc_start: 0.5605 (tpp) cc_final: 0.5344 (tpp) REVERT: D 474 MET cc_start: 0.0445 (tpt) cc_final: -0.0214 (tpp) REVERT: D 557 MET cc_start: 0.3490 (ttp) cc_final: 0.3046 (ptm) REVERT: D 581 VAL cc_start: 0.1036 (OUTLIER) cc_final: 0.0761 (m) REVERT: D 587 TYR cc_start: 0.0629 (t80) cc_final: 0.0004 (t80) REVERT: C 19 ARG cc_start: 0.6346 (ptp-170) cc_final: 0.5646 (mmt180) REVERT: C 104 TRP cc_start: 0.8118 (m-90) cc_final: 0.7803 (m100) REVERT: C 177 MET cc_start: 0.2406 (tpp) cc_final: 0.1850 (ttp) REVERT: C 242 LEU cc_start: 0.6901 (mp) cc_final: 0.6415 (tp) REVERT: C 284 THR cc_start: 0.8703 (m) cc_final: 0.8246 (p) REVERT: C 365 TYR cc_start: 0.8216 (m-80) cc_final: 0.7969 (m-10) REVERT: C 390 LEU cc_start: 0.8336 (mp) cc_final: 0.7616 (tp) REVERT: C 568 ASP cc_start: 0.7861 (p0) cc_final: 0.7553 (p0) REVERT: C 994 ASP cc_start: 0.8253 (t70) cc_final: 0.7895 (t0) REVERT: C 1072 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7982 (mt-10) outliers start: 117 outliers final: 88 residues processed: 414 average time/residue: 0.3942 time to fit residues: 269.1154 Evaluate side-chains 396 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 305 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1146 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 3.9990 chunk 328 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 364 optimal weight: 0.9980 chunk 302 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 B 245 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 957 GLN C1002 GLN C1106 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.5823 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= 0.211 Angle : 0.546 7.548 41396 Z= 0.283 Chirality : 0.043 0.247 4616 Planarity : 0.004 0.044 5375 Dihedral : 4.355 25.993 4050 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.42 % Allowed : 17.17 % Favored : 79.41 % 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: -0.47 (0.14), residues: 3733 helix: 1.37 (0.17), residues: 1001 sheet: -0.40 (0.19), residues: 681 loop : -1.16 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 478 HIS 0.005 0.001 HIS D 540 PHE 0.017 0.002 PHE A 486 TYR 0.022 0.001 TYR D 237 ARG 0.006 0.000 ARG B 567 *********************** 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: 113 poor density : 340 time to evaluate : 3.311 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 128 ILE cc_start: 0.9308 (mp) cc_final: 0.8999 (pt) REVERT: B 223 LEU cc_start: 0.8071 (mp) cc_final: 0.7660 (mt) REVERT: B 297 SER cc_start: 0.8854 (m) cc_final: 0.8368 (t) REVERT: B 403 ARG cc_start: 0.4243 (mtm180) cc_final: 0.3974 (mtp85) REVERT: B 408 ARG cc_start: 0.4740 (OUTLIER) cc_final: 0.4396 (tmm-80) REVERT: B 456 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7300 (m-10) REVERT: B 458 LYS cc_start: 0.6567 (mptt) cc_final: 0.5883 (pttm) REVERT: B 752 LEU cc_start: 0.9555 (tp) cc_final: 0.9085 (tp) REVERT: B 900 MET cc_start: 0.8640 (mmt) cc_final: 0.8062 (mpp) REVERT: B 957 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7795 (tm-30) REVERT: A 110 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6864 (mm) REVERT: A 178 ASP cc_start: 0.6250 (p0) cc_final: 0.5172 (p0) REVERT: A 269 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.5733 (m-80) REVERT: A 780 GLU cc_start: 0.8340 (tt0) cc_final: 0.8121 (tt0) REVERT: A 856 ASN cc_start: 0.8423 (t0) cc_final: 0.8074 (m110) REVERT: A 925 ASN cc_start: 0.8429 (m-40) cc_final: 0.7983 (m-40) REVERT: A 957 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7589 (tm-30) REVERT: A 1110 TYR cc_start: 0.8856 (t80) cc_final: 0.8402 (t80) REVERT: D 192 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7900 (ttp80) REVERT: D 202 TYR cc_start: 0.6448 (t80) cc_final: 0.6096 (m-80) REVERT: D 323 MET cc_start: 0.3339 (mmt) cc_final: 0.2744 (mpp) REVERT: D 408 MET cc_start: 0.5581 (tpp) cc_final: 0.5316 (tpp) REVERT: D 474 MET cc_start: -0.0085 (tpt) cc_final: -0.0815 (tpp) REVERT: D 557 MET cc_start: 0.3412 (ttp) cc_final: 0.2973 (ptm) REVERT: D 573 VAL cc_start: 0.3468 (t) cc_final: 0.2712 (m) REVERT: D 579 MET cc_start: -0.0581 (mmt) cc_final: -0.0795 (mmm) REVERT: D 581 VAL cc_start: 0.1345 (OUTLIER) cc_final: 0.0990 (m) REVERT: C 19 ARG cc_start: 0.6295 (ptp-170) cc_final: 0.5648 (mmp80) REVERT: C 55 PHE cc_start: 0.8096 (m-80) cc_final: 0.7206 (m-80) REVERT: C 104 TRP cc_start: 0.8096 (m-90) cc_final: 0.7765 (m100) REVERT: C 177 MET cc_start: 0.2180 (tpp) cc_final: 0.1775 (ttp) REVERT: C 242 LEU cc_start: 0.7096 (mp) cc_final: 0.6574 (tp) REVERT: C 284 THR cc_start: 0.8607 (m) cc_final: 0.8154 (p) REVERT: C 365 TYR cc_start: 0.8247 (m-80) cc_final: 0.7977 (m-10) REVERT: C 568 ASP cc_start: 0.7842 (p0) cc_final: 0.7514 (p0) REVERT: C 585 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8864 (pp) REVERT: C 975 SER cc_start: 0.8922 (p) cc_final: 0.8613 (t) REVERT: C 994 ASP cc_start: 0.8189 (t70) cc_final: 0.7856 (t0) REVERT: C 1072 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7823 (mt-10) outliers start: 113 outliers final: 85 residues processed: 422 average time/residue: 0.3932 time to fit residues: 271.5016 Evaluate side-chains 405 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 313 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 704 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 738 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C 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: 2.9990 chunk 41 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 206 optimal weight: 0.7980 chunk 307 optimal weight: 7.9990 chunk 203 optimal weight: 0.7980 chunk 363 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 165 ASN C 450 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 957 GLN C1106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30444 Z= 0.176 Angle : 0.533 14.294 41396 Z= 0.274 Chirality : 0.042 0.165 4616 Planarity : 0.003 0.044 5375 Dihedral : 4.228 25.680 4050 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.48 % Allowed : 17.63 % Favored : 78.89 % 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: -0.39 (0.14), residues: 3733 helix: 1.41 (0.17), residues: 1012 sheet: -0.30 (0.19), residues: 646 loop : -1.11 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 168 HIS 0.008 0.001 HIS B 245 PHE 0.018 0.001 PHE B 32 TYR 0.022 0.001 TYR A 265 ARG 0.007 0.000 ARG D 169 *********************** 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 457 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 342 time to evaluate : 3.295 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 128 ILE cc_start: 0.9307 (mp) cc_final: 0.9042 (pt) REVERT: B 195 LYS cc_start: 0.7643 (pptt) cc_final: 0.6944 (ptpt) REVERT: B 223 LEU cc_start: 0.7973 (mp) cc_final: 0.7490 (mt) REVERT: B 228 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6688 (t70) REVERT: B 297 SER cc_start: 0.8877 (m) cc_final: 0.8372 (t) REVERT: B 403 ARG cc_start: 0.4250 (mtm180) cc_final: 0.3978 (mtp85) REVERT: B 408 ARG cc_start: 0.4732 (OUTLIER) cc_final: 0.4225 (tmm-80) REVERT: B 456 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: B 752 LEU cc_start: 0.9553 (tp) cc_final: 0.9058 (tp) REVERT: B 900 MET cc_start: 0.8624 (mmt) cc_final: 0.8102 (mtm) REVERT: B 957 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7757 (tm-30) REVERT: B 995 ARG cc_start: 0.8600 (mtp85) cc_final: 0.7973 (mtm-85) REVERT: A 110 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6950 (mm) REVERT: A 177 MET cc_start: -0.0602 (mmt) cc_final: -0.0864 (mmt) REVERT: A 269 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.5771 (m-80) REVERT: A 780 GLU cc_start: 0.8322 (tt0) cc_final: 0.8100 (tt0) REVERT: A 925 ASN cc_start: 0.8400 (m-40) cc_final: 0.7950 (m-40) REVERT: A 957 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 1110 TYR cc_start: 0.8838 (t80) cc_final: 0.8362 (t80) REVERT: D 202 TYR cc_start: 0.6381 (t80) cc_final: 0.6027 (m-80) REVERT: D 323 MET cc_start: 0.3534 (mmt) cc_final: 0.3053 (mpp) REVERT: D 408 MET cc_start: 0.5849 (tpp) cc_final: 0.5558 (tpt) REVERT: D 474 MET cc_start: 0.0190 (tpt) cc_final: -0.0573 (tpp) REVERT: D 557 MET cc_start: 0.3514 (ttp) cc_final: 0.3044 (ptm) REVERT: D 573 VAL cc_start: 0.3398 (t) cc_final: 0.2653 (m) REVERT: D 581 VAL cc_start: 0.1297 (OUTLIER) cc_final: 0.0946 (m) REVERT: C 19 ARG cc_start: 0.6087 (ptp-170) cc_final: 0.5521 (mmp80) REVERT: C 55 PHE cc_start: 0.8075 (m-80) cc_final: 0.7172 (m-80) REVERT: C 104 TRP cc_start: 0.8111 (m-90) cc_final: 0.7595 (m-90) REVERT: C 180 GLU cc_start: -0.1610 (OUTLIER) cc_final: -0.2181 (tp30) REVERT: C 242 LEU cc_start: 0.7223 (mp) cc_final: 0.6681 (tp) REVERT: C 284 THR cc_start: 0.8562 (m) cc_final: 0.8104 (p) REVERT: C 365 TYR cc_start: 0.8274 (m-80) cc_final: 0.8007 (m-10) REVERT: C 568 ASP cc_start: 0.7866 (p0) cc_final: 0.7591 (p0) REVERT: C 585 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8866 (pp) REVERT: C 975 SER cc_start: 0.8948 (p) cc_final: 0.8675 (m) REVERT: C 994 ASP cc_start: 0.8116 (t70) cc_final: 0.7828 (t0) REVERT: C 1072 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7788 (mt-10) outliers start: 115 outliers final: 88 residues processed: 425 average time/residue: 0.3959 time to fit residues: 275.6534 Evaluate side-chains 416 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 319 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C 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: 3.9990 chunk 145 optimal weight: 0.0170 chunk 217 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 285 optimal weight: 5.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30444 Z= 0.206 Angle : 0.552 13.031 41396 Z= 0.284 Chirality : 0.043 0.160 4616 Planarity : 0.004 0.044 5375 Dihedral : 4.303 25.790 4050 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.57 % Allowed : 17.93 % Favored : 78.50 % 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: -0.42 (0.14), residues: 3733 helix: 1.34 (0.17), residues: 1029 sheet: -0.32 (0.20), residues: 644 loop : -1.12 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 168 HIS 0.005 0.001 HIS D 540 PHE 0.030 0.002 PHE B 32 TYR 0.027 0.001 TYR C 904 ARG 0.006 0.000 ARG B 567 *********************** 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 450 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 332 time to evaluate : 3.634 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 128 ILE cc_start: 0.9320 (mp) cc_final: 0.9072 (pt) REVERT: B 195 LYS cc_start: 0.7695 (pptt) cc_final: 0.7005 (pttt) REVERT: B 223 LEU cc_start: 0.8132 (mp) cc_final: 0.7657 (mt) REVERT: B 297 SER cc_start: 0.8900 (m) cc_final: 0.8408 (t) REVERT: B 403 ARG cc_start: 0.4408 (mtm180) cc_final: 0.4081 (mtp85) REVERT: B 408 ARG cc_start: 0.4725 (OUTLIER) cc_final: 0.4341 (tmm-80) REVERT: B 456 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7311 (m-10) REVERT: B 900 MET cc_start: 0.8652 (mmt) cc_final: 0.8141 (mtm) REVERT: B 957 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7780 (tm-30) REVERT: A 110 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6874 (mm) REVERT: A 117 LEU cc_start: 0.8247 (tt) cc_final: 0.7846 (tt) REVERT: A 177 MET cc_start: -0.0868 (mmt) cc_final: -0.1142 (mmt) REVERT: A 265 TYR cc_start: 0.7075 (p90) cc_final: 0.6400 (p90) REVERT: A 269 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.5722 (m-80) REVERT: A 780 GLU cc_start: 0.8334 (tt0) cc_final: 0.8086 (tt0) REVERT: A 856 ASN cc_start: 0.8449 (t0) cc_final: 0.8079 (m110) REVERT: A 925 ASN cc_start: 0.8441 (m-40) cc_final: 0.8024 (m-40) REVERT: A 957 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 1110 TYR cc_start: 0.8846 (t80) cc_final: 0.8361 (t80) REVERT: D 202 TYR cc_start: 0.6389 (t80) cc_final: 0.6038 (m-80) REVERT: D 323 MET cc_start: 0.3693 (mmt) cc_final: 0.3274 (mpp) REVERT: D 408 MET cc_start: 0.5764 (tpp) cc_final: 0.5487 (tpp) REVERT: D 474 MET cc_start: 0.0341 (tpt) cc_final: -0.0484 (tpp) REVERT: D 557 MET cc_start: 0.3485 (ttp) cc_final: 0.3115 (ptm) REVERT: D 573 VAL cc_start: 0.3293 (t) cc_final: 0.2572 (m) REVERT: D 581 VAL cc_start: 0.1007 (OUTLIER) cc_final: 0.0760 (m) REVERT: C 19 ARG cc_start: 0.6232 (ptp-170) cc_final: 0.5699 (tpp-160) REVERT: C 55 PHE cc_start: 0.8089 (m-80) cc_final: 0.7202 (m-80) REVERT: C 104 TRP cc_start: 0.8111 (m-90) cc_final: 0.7814 (m100) REVERT: C 284 THR cc_start: 0.8585 (m) cc_final: 0.8127 (p) REVERT: C 365 TYR cc_start: 0.8270 (m-80) cc_final: 0.7975 (m-10) REVERT: C 568 ASP cc_start: 0.7894 (p0) cc_final: 0.7574 (p0) REVERT: C 585 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8864 (pp) REVERT: C 975 SER cc_start: 0.8916 (p) cc_final: 0.8693 (m) REVERT: C 994 ASP cc_start: 0.8183 (t70) cc_final: 0.7868 (t0) REVERT: C 1072 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7831 (mt-10) outliers start: 118 outliers final: 97 residues processed: 419 average time/residue: 0.3743 time to fit residues: 261.6458 Evaluate side-chains 412 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 308 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1146 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 6.9990 chunk 348 optimal weight: 0.1980 chunk 317 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 265 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 chunk 320 optimal weight: 0.0570 chunk 337 optimal weight: 3.9990 overall best weight: 2.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A1005 GLN D 34 HIS ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.6497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30444 Z= 0.275 Angle : 0.613 12.675 41396 Z= 0.316 Chirality : 0.044 0.177 4616 Planarity : 0.004 0.044 5375 Dihedral : 4.628 25.685 4050 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.73 % Allowed : 18.29 % Favored : 77.98 % 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: -0.57 (0.13), residues: 3733 helix: 1.20 (0.16), residues: 1033 sheet: -0.44 (0.20), residues: 638 loop : -1.20 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 168 HIS 0.011 0.001 HIS B 245 PHE 0.025 0.002 PHE B 927 TYR 0.021 0.002 TYR C 904 ARG 0.008 0.001 ARG C1107 *********************** 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 440 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 317 time to evaluate : 3.437 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 128 ILE cc_start: 0.9292 (mp) cc_final: 0.9003 (mp) REVERT: B 195 LYS cc_start: 0.7702 (pptt) cc_final: 0.7060 (ptpt) REVERT: B 223 LEU cc_start: 0.8167 (mp) cc_final: 0.7632 (mt) REVERT: B 297 SER cc_start: 0.8896 (m) cc_final: 0.8395 (t) REVERT: B 403 ARG cc_start: 0.4500 (mtm180) cc_final: 0.4111 (mtp85) REVERT: B 408 ARG cc_start: 0.4778 (OUTLIER) cc_final: 0.4281 (tmm-80) REVERT: B 456 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7326 (m-10) REVERT: B 900 MET cc_start: 0.8673 (mmt) cc_final: 0.8131 (mpp) REVERT: B 957 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7881 (tm-30) REVERT: A 117 LEU cc_start: 0.8312 (tt) cc_final: 0.7910 (tt) REVERT: A 177 MET cc_start: -0.1024 (mmt) cc_final: -0.1230 (mmt) REVERT: A 265 TYR cc_start: 0.7101 (p90) cc_final: 0.6418 (p90) REVERT: A 269 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.5728 (m-80) REVERT: A 703 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8300 (t0) REVERT: A 780 GLU cc_start: 0.8347 (tt0) cc_final: 0.8127 (tt0) REVERT: A 787 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8062 (pm20) REVERT: A 856 ASN cc_start: 0.8458 (t0) cc_final: 0.7973 (m110) REVERT: A 925 ASN cc_start: 0.8496 (m-40) cc_final: 0.8143 (m-40) REVERT: A 957 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 1110 TYR cc_start: 0.8864 (t80) cc_final: 0.8364 (t80) REVERT: D 202 TYR cc_start: 0.6322 (t80) cc_final: 0.5959 (m-80) REVERT: D 323 MET cc_start: 0.3561 (mmt) cc_final: 0.3174 (mpp) REVERT: D 408 MET cc_start: 0.5813 (tpp) cc_final: 0.5566 (tpp) REVERT: D 474 MET cc_start: 0.0816 (tpt) cc_final: 0.0344 (tpt) REVERT: D 557 MET cc_start: 0.3512 (ttp) cc_final: 0.3080 (ptm) REVERT: D 573 VAL cc_start: 0.3412 (t) cc_final: 0.2703 (m) REVERT: D 581 VAL cc_start: 0.1022 (OUTLIER) cc_final: 0.0775 (m) REVERT: C 19 ARG cc_start: 0.6290 (ptp-170) cc_final: 0.5609 (mmp80) REVERT: C 104 TRP cc_start: 0.8177 (m-90) cc_final: 0.7830 (m100) REVERT: C 180 GLU cc_start: -0.0471 (OUTLIER) cc_final: -0.1163 (tp30) REVERT: C 284 THR cc_start: 0.8610 (m) cc_final: 0.8160 (p) REVERT: C 365 TYR cc_start: 0.8257 (m-80) cc_final: 0.7888 (m-10) REVERT: C 568 ASP cc_start: 0.7929 (p0) cc_final: 0.7554 (p0) REVERT: C 585 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8817 (pp) REVERT: C 994 ASP cc_start: 0.8285 (t70) cc_final: 0.7742 (t0) REVERT: C 1072 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7882 (mt-10) outliers start: 123 outliers final: 104 residues processed: 409 average time/residue: 0.3934 time to fit residues: 265.6010 Evaluate side-chains 413 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 300 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1146 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 10.0000 chunk 358 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 375 optimal weight: 0.5980 chunk 345 optimal weight: 0.6980 chunk 299 optimal weight: 2.9990 chunk 31 optimal weight: 0.0050 chunk 231 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 30444 Z= 0.154 Angle : 0.548 13.795 41396 Z= 0.279 Chirality : 0.043 0.250 4616 Planarity : 0.004 0.045 5375 Dihedral : 4.230 24.713 4050 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.57 % Allowed : 19.72 % Favored : 77.71 % 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: -0.36 (0.14), residues: 3733 helix: 1.50 (0.17), residues: 1023 sheet: -0.34 (0.19), residues: 672 loop : -1.13 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 168 HIS 0.007 0.001 HIS B 245 PHE 0.025 0.001 PHE B 32 TYR 0.019 0.001 TYR B 396 ARG 0.010 0.000 ARG A1019 ********************** 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 435 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 350 time to evaluate : 3.637 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 195 LYS cc_start: 0.7623 (pptt) cc_final: 0.7124 (pttt) REVERT: B 223 LEU cc_start: 0.8177 (mp) cc_final: 0.7708 (mt) REVERT: B 297 SER cc_start: 0.8896 (m) cc_final: 0.8355 (t) REVERT: B 403 ARG cc_start: 0.4294 (mtm180) cc_final: 0.3944 (mtp85) REVERT: B 408 ARG cc_start: 0.4890 (OUTLIER) cc_final: 0.4305 (tmm-80) REVERT: B 456 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7254 (m-10) REVERT: B 752 LEU cc_start: 0.9599 (tp) cc_final: 0.9165 (tp) REVERT: B 900 MET cc_start: 0.8599 (mmt) cc_final: 0.8182 (mtm) REVERT: B 957 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 233 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7609 (tt) REVERT: A 265 TYR cc_start: 0.7129 (p90) cc_final: 0.6520 (p90) REVERT: A 269 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.5479 (m-80) REVERT: A 703 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8431 (t0) REVERT: A 780 GLU cc_start: 0.8354 (tt0) cc_final: 0.8146 (tt0) REVERT: A 856 ASN cc_start: 0.8449 (t0) cc_final: 0.8088 (m110) REVERT: A 925 ASN cc_start: 0.8387 (m-40) cc_final: 0.7967 (m-40) REVERT: A 957 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 1110 TYR cc_start: 0.8802 (t80) cc_final: 0.8326 (t80) REVERT: D 202 TYR cc_start: 0.6438 (t80) cc_final: 0.6079 (m-80) REVERT: D 323 MET cc_start: 0.3602 (mmt) cc_final: 0.3239 (mpp) REVERT: D 408 MET cc_start: 0.5803 (tpp) cc_final: 0.5547 (tpp) REVERT: D 474 MET cc_start: 0.0114 (tpt) cc_final: -0.0636 (tpp) REVERT: D 557 MET cc_start: 0.3219 (ttp) cc_final: 0.2833 (ptm) REVERT: D 573 VAL cc_start: 0.3415 (t) cc_final: 0.2703 (m) REVERT: C 19 ARG cc_start: 0.5960 (ptp-170) cc_final: 0.5611 (mmp80) REVERT: C 55 PHE cc_start: 0.8100 (m-80) cc_final: 0.7173 (m-80) REVERT: C 92 PHE cc_start: 0.8186 (m-80) cc_final: 0.7643 (t80) REVERT: C 104 TRP cc_start: 0.8246 (m-90) cc_final: 0.7757 (m100) REVERT: C 284 THR cc_start: 0.8600 (m) cc_final: 0.8157 (p) REVERT: C 365 TYR cc_start: 0.8341 (m-80) cc_final: 0.8039 (m-10) REVERT: C 568 ASP cc_start: 0.8048 (p0) cc_final: 0.7721 (p0) REVERT: C 585 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8879 (pp) REVERT: C 726 ILE cc_start: 0.9176 (mp) cc_final: 0.8857 (mt) REVERT: C 764 ASN cc_start: 0.8142 (m-40) cc_final: 0.7812 (m110) REVERT: C 994 ASP cc_start: 0.8060 (t70) cc_final: 0.7797 (t0) REVERT: C 1072 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7739 (mt-10) outliers start: 85 outliers final: 68 residues processed: 409 average time/residue: 0.4129 time to fit residues: 281.0408 Evaluate side-chains 395 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 320 time to evaluate : 5.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 8.9990 chunk 318 optimal weight: 0.0270 chunk 91 optimal weight: 0.9990 chunk 275 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 299 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 307 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- 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 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN A 703 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.138555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.111327 restraints weight = 99978.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113489 restraints weight = 49384.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.114285 restraints weight = 31480.436| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30444 Z= 0.153 Angle : 0.552 13.841 41396 Z= 0.280 Chirality : 0.043 0.252 4616 Planarity : 0.004 0.046 5375 Dihedral : 4.101 24.668 4050 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.48 % Allowed : 19.93 % Favored : 77.59 % 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: -0.23 (0.14), residues: 3733 helix: 1.59 (0.17), residues: 1028 sheet: -0.20 (0.19), residues: 676 loop : -1.08 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 168 HIS 0.009 0.001 HIS B 245 PHE 0.025 0.001 PHE B 32 TYR 0.017 0.001 TYR B 396 ARG 0.009 0.000 ARG A1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6600.61 seconds wall clock time: 120 minutes 42.60 seconds (7242.60 seconds total)