Starting phenix.real_space_refine on Tue Feb 20 14:43:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9e_32365/02_2024/7w9e_32365.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9e_32365/02_2024/7w9e_32365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9e_32365/02_2024/7w9e_32365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9e_32365/02_2024/7w9e_32365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9e_32365/02_2024/7w9e_32365.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9e_32365/02_2024/7w9e_32365.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.075 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 128 5.16 5 C 17935 2.51 5 N 4723 2.21 5 O 5395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "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 TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "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 ASP 571": "OD1" <-> "OD2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "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 TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "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 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 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "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 TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C 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 707": "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 TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ASP 57": "OD1" <-> "OD2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 143": "OD1" <-> "OD2" Residue "E ASP 165": "OD1" <-> "OD2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28181 Number of models: 1 Model: "" Number of chains: 5 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: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "C" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "D" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1671 Classifications: {'peptide': 220} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 202} Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1643 Classifications: {'peptide': 211} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 200} Time building chain proxies: 13.59, per 1000 atoms: 0.48 Number of scatterers: 28181 At special positions: 0 Unit cell: (157.392, 144.276, 260.134, 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 128 16.00 O 5395 8.00 N 4723 7.00 C 17935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 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=2.04 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " 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: 9.45 Conformation dependent library (CDL) restraints added in 5.0 seconds 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6748 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 63 sheets defined 21.1% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... 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 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.114A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.658A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 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: 3.817A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.553A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.819A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.551A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.847A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.800A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.500A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.758A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.208A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.208A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.514A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.560A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.551A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.612A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.731A 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: 3.733A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (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 977 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.234A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.129A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.536A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.544A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.976A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.548A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.507A 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: 3.651A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.706A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.555A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.918A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.602A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.508A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.974A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.122A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.457A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing helix chain 'D' and resid 62 through 65 removed outlier: 4.070A pdb=" N LYS D 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 90 removed outlier: 3.627A pdb=" N ASP D 90 " --> pdb=" O THR D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.627A pdb=" N TYR D 104 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.796A pdb=" N LEU E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.548A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 67 removed outlier: 4.245A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 67 removed outlier: 4.245A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.566A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.407A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.533A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.826A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.826A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.996A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.093A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.576A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.247A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.791A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 30 removed outlier: 4.573A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.919A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.996A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.537A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.798A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.615A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.520A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.512A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.530A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.148A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.599A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 721 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 721 removed outlier: 3.605A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.297A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.783A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.297A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.568A pdb=" N TYR C 279 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.025A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.501A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.634A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.554A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.124A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.673A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.367A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.758A pdb=" N VAL D 18 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS D 22 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.558A pdb=" N GLU D 10 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 117 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER D 40 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU D 45 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 50 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 59 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.658A pdb=" N VAL D 143 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 188 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS D 147 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 186 " --> pdb=" O CYS D 147 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 184 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR D 182 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.658A pdb=" N VAL D 143 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 188 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS D 147 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 186 " --> pdb=" O CYS D 147 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 184 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR D 182 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.664A pdb=" N THR D 211 " --> pdb=" O HIS D 206 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.675A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 72 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AG7, first strand: chain 'E' and resid 45 through 49 removed outlier: 6.729A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR E 49 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.841A pdb=" N ASN E 137 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 153 through 154 removed outlier: 3.792A pdb=" N ASN E 145 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 149 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) 1003 hydrogen bonds defined for protein. 2718 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: 13.15 Time building geometry restraints manager: 10.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9107 1.34 - 1.46: 7138 1.46 - 1.59: 12425 1.59 - 1.71: 0 1.71 - 1.83: 164 Bond restraints: 28834 Sorted by residual: bond pdb=" N GLN C 14 " pdb=" CA GLN C 14 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.29e+00 bond pdb=" N GLN A 14 " pdb=" CA GLN A 14 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N GLN B 14 " pdb=" CA GLN B 14 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" CA PRO D 133 " pdb=" C PRO D 133 " ideal model delta sigma weight residual 1.516 1.539 -0.022 1.42e-02 4.96e+03 2.49e+00 bond pdb=" N THR E 51 " pdb=" CA THR E 51 " ideal model delta sigma weight residual 1.462 1.484 -0.022 1.48e-02 4.57e+03 2.29e+00 ... (remaining 28829 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.91: 632 105.91 - 112.94: 15324 112.94 - 119.97: 9399 119.97 - 127.00: 13565 127.00 - 134.03: 303 Bond angle restraints: 39223 Sorted by residual: angle pdb=" C PRO D 133 " pdb=" N GLY D 134 " pdb=" CA GLY D 134 " ideal model delta sigma weight residual 121.70 132.38 -10.68 1.80e+00 3.09e-01 3.52e+01 angle pdb=" C SER E 50 " pdb=" N THR E 51 " pdb=" CA THR E 51 " ideal model delta sigma weight residual 122.61 129.73 -7.12 1.56e+00 4.11e-01 2.08e+01 angle pdb=" CA PRO D 133 " pdb=" C PRO D 133 " pdb=" N GLY D 134 " ideal model delta sigma weight residual 117.98 123.80 -5.82 1.43e+00 4.89e-01 1.65e+01 angle pdb=" N PRO D 133 " pdb=" CA PRO D 133 " pdb=" C PRO D 133 " ideal model delta sigma weight residual 113.40 118.54 -5.14 1.34e+00 5.57e-01 1.47e+01 angle pdb=" N LYS C 97 " pdb=" CA LYS C 97 " pdb=" C LYS C 97 " ideal model delta sigma weight residual 113.43 109.36 4.07 1.26e+00 6.30e-01 1.04e+01 ... (remaining 39218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 15882 17.87 - 35.74: 1096 35.74 - 53.61: 160 53.61 - 71.48: 35 71.48 - 89.35: 29 Dihedral angle restraints: 17202 sinusoidal: 6702 harmonic: 10500 Sorted by residual: dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 140.40 -47.40 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CA TYR D 105 " pdb=" C TYR D 105 " pdb=" N ALA D 106 " pdb=" CA ALA D 106 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" SG CYS C 738 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " pdb=" CA CYS C 760 " ideal model delta sinusoidal sigma weight residual -73.00 -5.18 -67.82 1 2.00e+01 2.50e-03 1.49e+01 ... (remaining 17199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3538 0.047 - 0.094: 591 0.094 - 0.141: 284 0.141 - 0.188: 8 0.188 - 0.236: 3 Chirality restraints: 4424 Sorted by residual: chirality pdb=" CA PRO D 133 " pdb=" N PRO D 133 " pdb=" C PRO D 133 " pdb=" CB PRO D 133 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA THR E 51 " pdb=" N THR E 51 " pdb=" C THR E 51 " pdb=" CB THR E 51 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 4421 not shown) Planarity restraints: 5084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 101 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO D 102 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 155 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO D 156 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 132 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.53e+00 pdb=" N PRO D 133 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 133 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 133 " -0.026 5.00e-02 4.00e+02 ... (remaining 5081 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 266 2.60 - 3.18: 23314 3.18 - 3.75: 41062 3.75 - 4.33: 58897 4.33 - 4.90: 98243 Nonbonded interactions: 221782 Sorted by model distance: nonbonded pdb=" CE LYS C 478 " pdb=" CE1 TYR E 96 " model vdw 2.028 3.740 nonbonded pdb=" OE1 GLN A 965 " pdb=" OG SER A1003 " model vdw 2.078 2.440 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.080 2.440 nonbonded pdb=" OG SER A 968 " pdb=" O GLN B 755 " model vdw 2.100 2.440 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.105 2.440 ... (remaining 221777 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 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: 14.350 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 71.890 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28834 Z= 0.246 Angle : 0.584 10.678 39223 Z= 0.311 Chirality : 0.044 0.236 4424 Planarity : 0.004 0.048 5084 Dihedral : 12.891 89.351 10325 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % 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: -3.93 (0.11), residues: 3565 helix: -2.78 (0.13), residues: 659 sheet: -2.51 (0.15), residues: 851 loop : -2.65 (0.11), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 195 HIS 0.004 0.001 HIS A1083 PHE 0.012 0.001 PHE E 139 TYR 0.011 0.001 TYR C 144 ARG 0.005 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 555 time to evaluate : 2.965 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: A 790 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7777 (mmmm) REVERT: B 521 PRO cc_start: 0.6758 (Cg_exo) cc_final: 0.6525 (Cg_endo) REVERT: B 735 SER cc_start: 0.8408 (t) cc_final: 0.8127 (p) REVERT: C 105 ILE cc_start: 0.8179 (mt) cc_final: 0.7935 (pt) REVERT: C 200 TYR cc_start: 0.5499 (m-80) cc_final: 0.5220 (m-10) REVERT: C 212 LEU cc_start: 0.6130 (tp) cc_final: 0.5855 (mt) REVERT: C 338 PHE cc_start: 0.6867 (m-80) cc_final: 0.6642 (m-80) REVERT: C 342 PHE cc_start: 0.7601 (m-80) cc_final: 0.6559 (m-80) REVERT: C 1005 GLN cc_start: 0.7521 (mt0) cc_final: 0.7215 (mt0) outliers start: 0 outliers final: 0 residues processed: 555 average time/residue: 0.4181 time to fit residues: 357.5277 Evaluate side-chains 271 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 327 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 137 ASN A 165 ASN A 196 ASN A 751 ASN A 950 ASN A 978 ASN B 115 GLN B 354 ASN B 370 ASN B 414 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1002 GLN C 14 GLN C 165 ASN C 414 GLN C 487 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1071 GLN D 5 GLN D 112 GLN D 140 ASN E 8 GLN E 145 ASN E 161 ASN E 166 GLN E 190 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28834 Z= 0.261 Angle : 0.580 9.880 39223 Z= 0.306 Chirality : 0.046 0.181 4424 Planarity : 0.004 0.055 5084 Dihedral : 4.331 18.020 3874 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.49 % Allowed : 9.42 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % 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: -2.33 (0.13), residues: 3565 helix: -0.26 (0.19), residues: 676 sheet: -1.57 (0.16), residues: 885 loop : -2.03 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 64 HIS 0.004 0.001 HIS A 49 PHE 0.019 0.002 PHE C 541 TYR 0.021 0.002 TYR B1067 ARG 0.009 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 295 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 ASN cc_start: 0.6360 (OUTLIER) cc_final: 0.6150 (m-40) REVERT: C 270 LEU cc_start: 0.8056 (mt) cc_final: 0.7817 (mt) REVERT: C 369 TYR cc_start: 0.5839 (t80) cc_final: 0.5616 (t80) REVERT: C 481 ASN cc_start: 0.4400 (m-40) cc_final: 0.4026 (t0) REVERT: C 542 ASN cc_start: 0.7769 (t0) cc_final: 0.7542 (t0) REVERT: C 586 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: D 34 MET cc_start: 0.3260 (mpp) cc_final: 0.2560 (mtp) outliers start: 47 outliers final: 27 residues processed: 330 average time/residue: 0.4067 time to fit residues: 214.7300 Evaluate side-chains 244 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 215 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.0270 chunk 101 optimal weight: 0.7980 chunk 272 optimal weight: 0.7980 chunk 223 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 328 optimal weight: 0.0970 chunk 354 optimal weight: 0.9990 chunk 292 optimal weight: 0.8980 chunk 325 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN A1010 GLN B 354 ASN B 901 GLN B 914 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28834 Z= 0.145 Angle : 0.484 7.386 39223 Z= 0.252 Chirality : 0.043 0.201 4424 Planarity : 0.004 0.058 5084 Dihedral : 3.936 18.358 3874 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.74 % Allowed : 10.43 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % 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: -1.50 (0.13), residues: 3565 helix: 0.79 (0.20), residues: 676 sheet: -1.06 (0.16), residues: 926 loop : -1.63 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 436 HIS 0.008 0.001 HIS A 49 PHE 0.023 0.001 PHE A 32 TYR 0.015 0.001 TYR B1067 ARG 0.006 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 242 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.2375 (mmm) cc_final: -0.2604 (mmt) REVERT: A 468 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7316 (mm) REVERT: A 613 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: A 740 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8230 (ttt) REVERT: B 395 VAL cc_start: 0.7835 (t) cc_final: 0.7617 (m) REVERT: C 94 SER cc_start: 0.7330 (m) cc_final: 0.6932 (p) REVERT: C 125 ASN cc_start: 0.6263 (OUTLIER) cc_final: 0.6059 (m-40) REVERT: C 481 ASN cc_start: 0.4510 (m-40) cc_final: 0.4014 (t0) REVERT: C 586 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: C 869 MET cc_start: 0.8424 (mtp) cc_final: 0.8211 (mtp) REVERT: D 34 MET cc_start: 0.3216 (mpp) cc_final: 0.2588 (mtp) outliers start: 55 outliers final: 29 residues processed: 279 average time/residue: 0.3795 time to fit residues: 173.0110 Evaluate side-chains 229 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 195 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 165 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 156 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 329 optimal weight: 0.7980 chunk 348 optimal weight: 0.0030 chunk 172 optimal weight: 0.9980 chunk 312 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 913 GLN B 955 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 641 ASN C 804 GLN C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 28834 Z= 0.148 Angle : 0.466 8.418 39223 Z= 0.243 Chirality : 0.042 0.166 4424 Planarity : 0.003 0.052 5084 Dihedral : 3.821 17.285 3874 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.97 % Allowed : 11.51 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % 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: -1.16 (0.14), residues: 3565 helix: 1.20 (0.21), residues: 667 sheet: -0.77 (0.16), residues: 914 loop : -1.49 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 886 HIS 0.003 0.001 HIS A 49 PHE 0.023 0.001 PHE A 32 TYR 0.015 0.001 TYR B1067 ARG 0.005 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 215 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7906 (pt) REVERT: A 468 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7306 (mm) REVERT: A 613 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8040 (mp10) REVERT: C 40 ASP cc_start: 0.8019 (p0) cc_final: 0.7768 (p0) REVERT: C 94 SER cc_start: 0.7332 (m) cc_final: 0.6956 (p) REVERT: C 125 ASN cc_start: 0.6305 (OUTLIER) cc_final: 0.6066 (m-40) REVERT: C 177 MET cc_start: 0.0666 (ttt) cc_final: -0.0258 (ttp) REVERT: C 269 TYR cc_start: 0.7862 (m-80) cc_final: 0.7649 (m-80) REVERT: C 586 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7086 (m-30) REVERT: D 34 MET cc_start: 0.3407 (mpp) cc_final: 0.2785 (mtp) REVERT: D 81 MET cc_start: 0.2096 (tpp) cc_final: 0.1828 (mmm) outliers start: 62 outliers final: 38 residues processed: 261 average time/residue: 0.3617 time to fit residues: 157.4042 Evaluate side-chains 233 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 165 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 913 GLN A 955 ASN B 134 GLN B 314 GLN B 498 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN C 99 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28834 Z= 0.311 Angle : 0.586 10.680 39223 Z= 0.307 Chirality : 0.046 0.171 4424 Planarity : 0.004 0.062 5084 Dihedral : 4.478 20.560 3874 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.69 % Allowed : 12.43 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % 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: -1.19 (0.14), residues: 3565 helix: 1.18 (0.21), residues: 657 sheet: -0.71 (0.17), residues: 896 loop : -1.54 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 258 HIS 0.006 0.001 HIS A 49 PHE 0.023 0.002 PHE A 32 TYR 0.024 0.002 TYR B 28 ARG 0.005 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 193 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7195 (mm) REVERT: A 613 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: B 515 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.5852 (p90) REVERT: B 740 MET cc_start: 0.7097 (mtp) cc_final: 0.6638 (mtt) REVERT: C 40 ASP cc_start: 0.8111 (p0) cc_final: 0.7838 (p0) REVERT: C 53 ASP cc_start: 0.7367 (m-30) cc_final: 0.7093 (m-30) REVERT: C 125 ASN cc_start: 0.6264 (OUTLIER) cc_final: 0.5974 (m-40) REVERT: C 258 TRP cc_start: 0.2283 (m100) cc_final: 0.1926 (m100) REVERT: C 519 HIS cc_start: 0.5776 (OUTLIER) cc_final: 0.5256 (p90) REVERT: D 3 GLN cc_start: 0.4390 (pm20) cc_final: 0.3202 (pp30) REVERT: D 34 MET cc_start: 0.3523 (mpp) cc_final: 0.2944 (mtp) REVERT: D 81 MET cc_start: 0.1998 (tpp) cc_final: 0.1461 (tpp) outliers start: 85 outliers final: 59 residues processed: 263 average time/residue: 0.3826 time to fit residues: 166.1792 Evaluate side-chains 233 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 169 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 165 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 0.0030 chunk 314 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 349 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 913 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 658 ASN C 764 ASN C 957 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28834 Z= 0.166 Angle : 0.489 10.070 39223 Z= 0.254 Chirality : 0.043 0.175 4424 Planarity : 0.003 0.059 5084 Dihedral : 4.109 21.457 3874 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.25 % Allowed : 13.70 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % 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: -0.93 (0.14), residues: 3565 helix: 1.49 (0.21), residues: 656 sheet: -0.56 (0.17), residues: 902 loop : -1.40 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 258 HIS 0.002 0.001 HIS A 655 PHE 0.017 0.001 PHE A 32 TYR 0.043 0.001 TYR B 707 ARG 0.008 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 200 time to evaluate : 3.146 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: A 105 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7932 (pt) REVERT: A 468 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.7117 (mm) REVERT: A 613 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: B 133 PHE cc_start: 0.5366 (m-80) cc_final: 0.4983 (m-80) REVERT: C 40 ASP cc_start: 0.7973 (p0) cc_final: 0.7720 (p0) REVERT: C 53 ASP cc_start: 0.7282 (m-30) cc_final: 0.7014 (m-30) REVERT: C 94 SER cc_start: 0.7272 (m) cc_final: 0.6895 (p) REVERT: C 125 ASN cc_start: 0.6276 (OUTLIER) cc_final: 0.5915 (m-40) REVERT: C 519 HIS cc_start: 0.5908 (OUTLIER) cc_final: 0.5466 (p90) REVERT: C 586 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.6973 (m-30) REVERT: D 3 GLN cc_start: 0.4206 (pm20) cc_final: 0.2960 (pp30) REVERT: D 34 MET cc_start: 0.3558 (mpp) cc_final: 0.3159 (mtp) REVERT: D 81 MET cc_start: 0.1850 (tpp) cc_final: 0.1588 (tpp) outliers start: 71 outliers final: 42 residues processed: 253 average time/residue: 0.3601 time to fit residues: 152.7976 Evaluate side-chains 230 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 165 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 294 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 212 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 99 ASN B 314 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1088 HIS C 99 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 751 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28834 Z= 0.297 Angle : 0.567 11.055 39223 Z= 0.297 Chirality : 0.045 0.209 4424 Planarity : 0.004 0.056 5084 Dihedral : 4.537 22.099 3874 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.79 % Allowed : 13.35 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % 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: -1.07 (0.14), residues: 3565 helix: 1.32 (0.21), residues: 665 sheet: -0.61 (0.17), residues: 912 loop : -1.52 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 258 HIS 0.004 0.001 HIS A 49 PHE 0.018 0.002 PHE B 898 TYR 0.030 0.002 TYR B 707 ARG 0.008 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 183 time to evaluate : 3.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.7127 (mm) REVERT: A 613 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: A 740 MET cc_start: 0.8258 (ttt) cc_final: 0.8045 (ttt) REVERT: A 745 ASP cc_start: 0.6727 (OUTLIER) cc_final: 0.6484 (m-30) REVERT: B 213 VAL cc_start: 0.7867 (m) cc_final: 0.7651 (p) REVERT: B 515 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.5295 (p90) REVERT: C 40 ASP cc_start: 0.7968 (p0) cc_final: 0.7710 (p0) REVERT: C 53 ASP cc_start: 0.7307 (m-30) cc_final: 0.7005 (m-30) REVERT: C 125 ASN cc_start: 0.6263 (OUTLIER) cc_final: 0.5891 (m-40) REVERT: C 177 MET cc_start: 0.0649 (OUTLIER) cc_final: 0.0378 (tmt) REVERT: C 586 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7032 (m-30) REVERT: D 3 GLN cc_start: 0.4057 (pm20) cc_final: 0.2905 (pp30) REVERT: D 34 MET cc_start: 0.3241 (mpp) cc_final: 0.2743 (mtp) REVERT: D 81 MET cc_start: 0.1895 (tpp) cc_final: 0.1695 (tpp) outliers start: 88 outliers final: 56 residues processed: 255 average time/residue: 0.3646 time to fit residues: 157.0506 Evaluate side-chains 232 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 169 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 172 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 273 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 751 ASN C 957 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN E 166 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28834 Z= 0.159 Angle : 0.486 10.475 39223 Z= 0.253 Chirality : 0.042 0.176 4424 Planarity : 0.003 0.052 5084 Dihedral : 4.132 21.490 3874 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.97 % Allowed : 14.24 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % 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: -0.80 (0.14), residues: 3565 helix: 1.76 (0.22), residues: 648 sheet: -0.46 (0.17), residues: 920 loop : -1.39 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 258 HIS 0.002 0.001 HIS D 206 PHE 0.022 0.001 PHE A 32 TYR 0.039 0.001 TYR B 707 ARG 0.007 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 198 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7068 (mm) REVERT: A 613 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: A 740 MET cc_start: 0.8165 (ttt) cc_final: 0.7866 (ttt) REVERT: B 133 PHE cc_start: 0.5421 (m-80) cc_final: 0.5083 (m-80) REVERT: B 213 VAL cc_start: 0.7677 (m) cc_final: 0.7458 (p) REVERT: C 40 ASP cc_start: 0.7867 (p0) cc_final: 0.7601 (p0) REVERT: C 53 ASP cc_start: 0.7265 (m-30) cc_final: 0.6985 (m-30) REVERT: C 94 SER cc_start: 0.7278 (m) cc_final: 0.6894 (p) REVERT: C 125 ASN cc_start: 0.6251 (OUTLIER) cc_final: 0.5868 (m-40) REVERT: C 481 ASN cc_start: 0.4478 (m-40) cc_final: 0.4051 (t0) REVERT: C 586 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.6979 (m-30) REVERT: C 900 MET cc_start: 0.8477 (mmm) cc_final: 0.7937 (mtt) REVERT: D 3 GLN cc_start: 0.3950 (pm20) cc_final: 0.2807 (pp30) REVERT: D 81 MET cc_start: 0.1869 (tpp) cc_final: 0.1627 (tpp) REVERT: D 109 HIS cc_start: 0.1053 (OUTLIER) cc_final: 0.0059 (t-170) outliers start: 62 outliers final: 47 residues processed: 245 average time/residue: 0.3494 time to fit residues: 145.3065 Evaluate side-chains 241 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 189 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 165 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 0.4980 chunk 333 optimal weight: 0.7980 chunk 304 optimal weight: 0.5980 chunk 324 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 254 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 292 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 957 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28834 Z= 0.153 Angle : 0.480 10.716 39223 Z= 0.249 Chirality : 0.042 0.176 4424 Planarity : 0.003 0.051 5084 Dihedral : 4.016 19.513 3874 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.00 % Allowed : 14.36 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % 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: -0.68 (0.14), residues: 3565 helix: 1.80 (0.22), residues: 654 sheet: -0.40 (0.17), residues: 935 loop : -1.28 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 258 HIS 0.004 0.001 HIS C 245 PHE 0.022 0.001 PHE A 32 TYR 0.034 0.001 TYR B 707 ARG 0.007 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 192 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.7081 (mm) REVERT: A 613 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: B 133 PHE cc_start: 0.5424 (m-80) cc_final: 0.5077 (m-80) REVERT: B 213 VAL cc_start: 0.7669 (m) cc_final: 0.7446 (p) REVERT: C 40 ASP cc_start: 0.7865 (p0) cc_final: 0.7586 (p0) REVERT: C 53 ASP cc_start: 0.7248 (m-30) cc_final: 0.7031 (m-30) REVERT: C 94 SER cc_start: 0.7410 (m) cc_final: 0.7056 (p) REVERT: C 125 ASN cc_start: 0.6216 (OUTLIER) cc_final: 0.5966 (m-40) REVERT: C 481 ASN cc_start: 0.4527 (m-40) cc_final: 0.4044 (t0) REVERT: C 586 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.6957 (m-30) REVERT: C 900 MET cc_start: 0.8481 (mmm) cc_final: 0.7940 (mtt) REVERT: D 3 GLN cc_start: 0.4188 (pm20) cc_final: 0.3051 (pp30) REVERT: D 34 MET cc_start: 0.3621 (mpp) cc_final: 0.2887 (mtp) REVERT: D 81 MET cc_start: 0.1872 (tpp) cc_final: 0.1644 (tpp) REVERT: D 109 HIS cc_start: 0.0886 (OUTLIER) cc_final: -0.0041 (t-170) outliers start: 63 outliers final: 56 residues processed: 239 average time/residue: 0.3530 time to fit residues: 144.0530 Evaluate side-chains 248 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 187 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 165 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 10.0000 chunk 342 optimal weight: 0.6980 chunk 209 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 238 optimal weight: 0.6980 chunk 359 optimal weight: 4.9990 chunk 331 optimal weight: 0.8980 chunk 286 optimal weight: 8.9990 chunk 29 optimal weight: 0.1980 chunk 221 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 563 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 957 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28834 Z= 0.154 Angle : 0.479 10.926 39223 Z= 0.248 Chirality : 0.042 0.187 4424 Planarity : 0.003 0.050 5084 Dihedral : 3.963 19.567 3874 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.90 % Allowed : 14.55 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % 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: -0.61 (0.14), residues: 3565 helix: 1.84 (0.22), residues: 654 sheet: -0.36 (0.17), residues: 956 loop : -1.24 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 258 HIS 0.002 0.001 HIS D 206 PHE 0.021 0.001 PHE A 32 TYR 0.033 0.001 TYR B 707 ARG 0.007 0.000 ARG B 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 193 time to evaluate : 3.278 Fit side-chains revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7953 (pt) REVERT: A 468 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.7079 (mm) REVERT: A 613 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: B 133 PHE cc_start: 0.5401 (m-80) cc_final: 0.5069 (m-80) REVERT: B 213 VAL cc_start: 0.7674 (m) cc_final: 0.7440 (p) REVERT: B 403 ARG cc_start: 0.4812 (mtp-110) cc_final: 0.4330 (ttp80) REVERT: C 40 ASP cc_start: 0.7860 (p0) cc_final: 0.7575 (p0) REVERT: C 53 ASP cc_start: 0.7221 (m-30) cc_final: 0.7007 (m-30) REVERT: C 94 SER cc_start: 0.7332 (m) cc_final: 0.6985 (p) REVERT: C 125 ASN cc_start: 0.6198 (OUTLIER) cc_final: 0.5949 (m-40) REVERT: C 481 ASN cc_start: 0.4546 (m-40) cc_final: 0.4065 (t0) REVERT: C 586 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: C 900 MET cc_start: 0.8480 (mmm) cc_final: 0.7936 (mtt) REVERT: D 3 GLN cc_start: 0.4214 (pm20) cc_final: 0.3013 (pp30) REVERT: D 34 MET cc_start: 0.3529 (mpp) cc_final: 0.2756 (mtp) REVERT: D 109 HIS cc_start: 0.0873 (OUTLIER) cc_final: -0.0051 (t-170) REVERT: E 211 ARG cc_start: 0.4006 (ptp90) cc_final: 0.2402 (tpp80) outliers start: 60 outliers final: 52 residues processed: 238 average time/residue: 0.3525 time to fit residues: 142.6671 Evaluate side-chains 243 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 185 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 165 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 264 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 286 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 239 GLN A 354 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 901 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.119913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.091529 restraints weight = 88798.470| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.45 r_work: 0.3436 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28834 Z= 0.232 Angle : 0.524 11.167 39223 Z= 0.271 Chirality : 0.043 0.195 4424 Planarity : 0.004 0.050 5084 Dihedral : 4.200 21.568 3874 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.03 % Allowed : 14.65 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.09 % 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: -0.72 (0.14), residues: 3565 helix: 1.71 (0.21), residues: 661 sheet: -0.40 (0.17), residues: 925 loop : -1.31 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 258 HIS 0.003 0.001 HIS D 206 PHE 0.021 0.001 PHE A 32 TYR 0.035 0.001 TYR B 707 ARG 0.006 0.000 ARG B 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5781.21 seconds wall clock time: 106 minutes 32.50 seconds (6392.50 seconds total)