Starting phenix.real_space_refine on Fri Dec 15 00:50:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/12_2023/7w9b_32363.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/12_2023/7w9b_32363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/12_2023/7w9b_32363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/12_2023/7w9b_32363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/12_2023/7w9b_32363.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9b_32363/12_2023/7w9b_32363.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 18970 2.51 5 N 4982 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 198": "OD1" <-> "OD2" Residue "D ASP 228": "OD1" <-> "OD2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 389": "OD1" <-> "OD2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 428": "OD1" <-> "OD2" Residue "D ASP 442": "OD1" <-> "OD2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 571": "OD1" <-> "OD2" Residue "D ASP 586": "OD1" <-> "OD2" Residue "D PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 979": "OD1" <-> "OD2" Residue "D TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1127": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 29737 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "C" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "D" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Time building chain proxies: 15.21, per 1000 atoms: 0.51 Number of scatterers: 29737 At special positions: 0 Unit cell: (156.299, 171.601, 241.553, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 143 16.00 O 5642 8.00 N 4982 7.00 C 18970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.65 Conformation dependent library (CDL) restraints added in 5.2 seconds 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7076 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 49 sheets defined 30.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.733A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.440A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.512A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.891A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.556A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.526A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.802A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.532A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.679A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.776A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.833A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.733A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.623A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.574A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.571A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.727A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.711A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.618A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.552A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 3.679A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 53 removed outlier: 3.887A pdb=" N ALA A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 4.287A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.645A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.561A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.533A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix removed outlier: 3.715A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.736A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.001A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.607A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.945A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.521A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.923A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.524A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.608A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.052A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.718A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.824A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.518A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.607A pdb=" N ASN A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.875A pdb=" N THR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.141A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.818A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.463A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.766A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.546A pdb=" N ASN D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.627A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.761A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.596A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 780 removed outlier: 3.512A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 773 " --> pdb=" O GLY D 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.642A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.541A pdb=" N GLN D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR D 873 " --> pdb=" O MET D 869 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 883 " --> pdb=" O ALA D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 891 removed outlier: 4.079A pdb=" N GLY D 891 " --> pdb=" O PHE D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.840A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.605A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.573A pdb=" N ASN D 950 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.675A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D1002 " --> pdb=" O THR D 998 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D1016 " --> pdb=" O LEU D1012 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D1030 " --> pdb=" O ALA D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1147 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.987A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.039A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.627A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.457A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.202A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.015A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.403A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.359A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'B' and resid 721 through 722 Processing sheet with id=AB6, first strand: chain 'B' and resid 721 through 722 removed outlier: 3.784A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.793A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.688A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.501A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.681A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.231A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.543A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.549A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.365A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AD2, first strand: chain 'C' and resid 717 through 722 removed outlier: 6.922A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.596A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AD5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'A' and resid 131 through 134 removed outlier: 6.013A pdb=" N GLU A 140 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.252A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.966A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.601A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.838A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.847A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.343A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 324 through 327 removed outlier: 4.043A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.614A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'D' and resid 654 through 660 removed outlier: 6.283A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 673 " --> pdb=" O ILE D 693 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.690A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.803A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'D' and resid 1120 through 1122 1146 hydrogen bonds defined for protein. 3177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.35 Time building geometry restraints manager: 11.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9636 1.35 - 1.47: 7670 1.47 - 1.60: 12944 1.60 - 1.72: 0 1.72 - 1.84: 194 Bond restraints: 30444 Sorted by residual: bond pdb=" C PHE B 497 " pdb=" N GLN B 498 " ideal model delta sigma weight residual 1.327 1.358 -0.031 1.71e-02 3.42e+03 3.30e+00 bond pdb=" N SER A 19 " pdb=" CA SER A 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N GLN C 14 " pdb=" CA GLN C 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLN B 14 " pdb=" CA GLN B 14 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" N GLN D 14 " pdb=" CA GLN D 14 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 ... (remaining 30439 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.41: 825 106.41 - 113.33: 16212 113.33 - 120.25: 10460 120.25 - 127.16: 13562 127.16 - 134.08: 337 Bond angle restraints: 41396 Sorted by residual: angle pdb=" N ILE B 410 " pdb=" CA ILE B 410 " pdb=" C ILE B 410 " ideal model delta sigma weight residual 106.21 109.52 -3.31 1.07e+00 8.73e-01 9.57e+00 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 112.12 109.54 2.58 8.40e-01 1.42e+00 9.42e+00 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.46 126.27 -3.81 1.41e+00 5.03e-01 7.29e+00 angle pdb=" C LEU B 916 " pdb=" CA LEU B 916 " pdb=" CB LEU B 916 " ideal model delta sigma weight residual 110.96 107.45 3.51 1.54e+00 4.22e-01 5.20e+00 angle pdb=" C GLU A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta sigma weight residual 127.00 132.42 -5.42 2.40e+00 1.74e-01 5.11e+00 ... (remaining 41391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 16876 17.80 - 35.59: 1022 35.59 - 53.39: 163 53.39 - 71.18: 54 71.18 - 88.98: 21 Dihedral angle restraints: 18136 sinusoidal: 7139 harmonic: 10997 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -125.67 39.67 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual -86.00 -47.04 -38.96 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 127.72 -34.72 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 18133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3303 0.037 - 0.074: 899 0.074 - 0.112: 290 0.112 - 0.149: 120 0.149 - 0.186: 4 Chirality restraints: 4616 Sorted by residual: chirality pdb=" CA ILE D 896 " pdb=" N ILE D 896 " pdb=" C ILE D 896 " pdb=" CB ILE D 896 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA ILE C 896 " pdb=" N ILE C 896 " pdb=" C ILE C 896 " pdb=" CB ILE C 896 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA ILE D 714 " pdb=" N ILE D 714 " pdb=" C ILE D 714 " pdb=" CB ILE D 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 4613 not shown) Planarity restraints: 5375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D1068 " -0.023 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO D1069 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO D1069 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D1069 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 896 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO D 897 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 897 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 897 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO B 521 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.018 5.00e-02 4.00e+02 ... (remaining 5372 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 292 2.63 - 3.19: 25876 3.19 - 3.76: 43714 3.76 - 4.33: 63049 4.33 - 4.90: 103930 Nonbonded interactions: 236861 Sorted by model distance: nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.057 2.440 nonbonded pdb=" OG1 THR B 883 " pdb=" OH TYR C 707 " model vdw 2.058 2.440 nonbonded pdb=" O GLN C 755 " pdb=" OG SER D 968 " model vdw 2.064 2.440 nonbonded pdb=" O GLN B 755 " pdb=" OG SER C 968 " model vdw 2.077 2.440 nonbonded pdb=" OE1 GLN B 965 " pdb=" OG SER B1003 " model vdw 2.131 2.440 ... (remaining 236856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.040 Extract box with map and model: 11.060 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 77.510 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30444 Z= 0.239 Angle : 0.582 6.493 41396 Z= 0.325 Chirality : 0.042 0.186 4616 Planarity : 0.003 0.034 5375 Dihedral : 12.343 88.980 10934 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.03 % Allowed : 1.27 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.11), residues: 3733 helix: -2.50 (0.11), residues: 1023 sheet: -2.08 (0.17), residues: 643 loop : -2.18 (0.11), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 203 HIS 0.004 0.001 HIS A 540 PHE 0.011 0.001 PHE C1075 TYR 0.014 0.001 TYR D 707 ARG 0.003 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 762 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 763 average time/residue: 0.4428 time to fit residues: 523.2812 Evaluate side-chains 361 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 3.352 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2488 time to fit residues: 4.7921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 0.0050 chunk 285 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 295 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 179 optimal weight: 0.5980 chunk 219 optimal weight: 9.9990 chunk 342 optimal weight: 3.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN B 394 ASN B 474 GLN B 556 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 148 ASN C 334 ASN C 437 ASN C 703 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 914 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN A 103 ASN A 121 ASN A 429 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 134 GLN D 218 GLN D 394 ASN D 641 ASN D 787 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 30444 Z= 0.251 Angle : 0.583 8.724 41396 Z= 0.305 Chirality : 0.045 0.202 4616 Planarity : 0.004 0.047 5375 Dihedral : 4.077 21.388 4050 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.21 % Allowed : 10.05 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.12), residues: 3733 helix: -0.25 (0.15), residues: 1035 sheet: -1.28 (0.17), residues: 729 loop : -1.47 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 203 HIS 0.008 0.001 HIS A 195 PHE 0.019 0.002 PHE C 201 TYR 0.021 0.002 TYR A 381 ARG 0.006 0.001 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 439 time to evaluate : 4.524 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 outliers start: 73 outliers final: 44 residues processed: 491 average time/residue: 0.3948 time to fit residues: 317.2371 Evaluate side-chains 361 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 317 time to evaluate : 3.214 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2808 time to fit residues: 26.8923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 342 optimal weight: 0.8980 chunk 370 optimal weight: 0.5980 chunk 305 optimal weight: 3.9990 chunk 340 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 360 ASN B 703 ASN B 755 GLN C 437 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C 965 GLN C1142 GLN A 58 ASN A 139 GLN A 417 HIS A 522 GLN D 218 GLN D 394 ASN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 30444 Z= 0.256 Angle : 0.582 11.162 41396 Z= 0.302 Chirality : 0.045 0.161 4616 Planarity : 0.004 0.047 5375 Dihedral : 4.278 23.962 4050 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.03 % Allowed : 13.08 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 3733 helix: 0.51 (0.16), residues: 1038 sheet: -0.81 (0.18), residues: 749 loop : -1.28 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 610 HIS 0.006 0.001 HIS A 374 PHE 0.020 0.002 PHE B 32 TYR 0.034 0.002 TYR B 495 ARG 0.007 0.001 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 380 time to evaluate : 3.541 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 outliers start: 67 outliers final: 37 residues processed: 430 average time/residue: 0.4005 time to fit residues: 285.4502 Evaluate side-chains 334 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 297 time to evaluate : 3.187 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2893 time to fit residues: 23.9880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 344 optimal weight: 0.9990 chunk 364 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 326 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 655 HIS B 703 ASN B 804 GLN B 901 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS D 370 ASN D 655 HIS D 762 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 992 GLN D1106 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30444 Z= 0.192 Angle : 0.525 8.998 41396 Z= 0.272 Chirality : 0.043 0.194 4616 Planarity : 0.003 0.057 5375 Dihedral : 4.109 19.455 4050 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.45 % Allowed : 14.99 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 3733 helix: 0.92 (0.17), residues: 1024 sheet: -0.53 (0.18), residues: 749 loop : -1.04 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 69 HIS 0.005 0.001 HIS A 374 PHE 0.020 0.001 PHE D 106 TYR 0.047 0.001 TYR B 495 ARG 0.008 0.001 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 349 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 27 residues processed: 375 average time/residue: 0.3942 time to fit residues: 245.1855 Evaluate side-chains 327 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 300 time to evaluate : 3.273 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2901 time to fit residues: 18.9772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 5.9990 chunk 206 optimal weight: 0.0980 chunk 5 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 327 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 703 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 ASN A 96 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS D 173 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 30444 Z= 0.375 Angle : 0.659 16.443 41396 Z= 0.344 Chirality : 0.047 0.280 4616 Planarity : 0.004 0.064 5375 Dihedral : 4.895 24.921 4050 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.18 % Allowed : 15.87 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 3733 helix: 0.58 (0.16), residues: 1011 sheet: -0.44 (0.19), residues: 723 loop : -1.23 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 258 HIS 0.007 0.001 HIS A 374 PHE 0.025 0.002 PHE B 168 TYR 0.040 0.002 TYR A 41 ARG 0.009 0.001 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 321 time to evaluate : 3.218 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 outliers start: 72 outliers final: 38 residues processed: 374 average time/residue: 0.4127 time to fit residues: 256.6103 Evaluate side-chains 320 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 282 time to evaluate : 3.297 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.3036 time to fit residues: 26.6854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 5.9990 chunk 328 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 364 optimal weight: 0.6980 chunk 302 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN B 703 ASN B 804 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1002 GLN B1005 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 913 GLN C 926 GLN C 969 ASN ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 ASN A 401 HIS D 115 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 30444 Z= 0.211 Angle : 0.554 14.938 41396 Z= 0.287 Chirality : 0.044 0.225 4616 Planarity : 0.004 0.048 5375 Dihedral : 4.546 29.635 4050 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 17.44 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3733 helix: 0.85 (0.17), residues: 1012 sheet: -0.35 (0.19), residues: 724 loop : -1.11 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 258 HIS 0.005 0.001 HIS A 374 PHE 0.024 0.001 PHE B 338 TYR 0.031 0.002 TYR C 351 ARG 0.006 0.001 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 328 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 17 residues processed: 354 average time/residue: 0.4049 time to fit residues: 237.7020 Evaluate side-chains 308 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 291 time to evaluate : 3.260 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2843 time to fit residues: 13.4297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 266 optimal weight: 8.9990 chunk 206 optimal weight: 0.7980 chunk 307 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 363 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 370 ASN B 519 HIS B 540 ASN B 703 ASN B 804 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 969 ASN ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN A 49 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 30444 Z= 0.419 Angle : 0.693 13.754 41396 Z= 0.362 Chirality : 0.048 0.217 4616 Planarity : 0.005 0.063 5375 Dihedral : 5.279 27.524 4050 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.64 % Allowed : 17.87 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 3733 helix: 0.36 (0.16), residues: 1020 sheet: -0.45 (0.19), residues: 737 loop : -1.32 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 258 HIS 0.010 0.002 HIS A 373 PHE 0.024 0.002 PHE C 392 TYR 0.056 0.002 TYR B 707 ARG 0.008 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 296 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 27 residues processed: 334 average time/residue: 0.3918 time to fit residues: 219.3462 Evaluate side-chains 306 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 279 time to evaluate : 3.355 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2829 time to fit residues: 19.1541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 231 optimal weight: 0.0010 chunk 247 optimal weight: 9.9990 chunk 179 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 285 optimal weight: 0.7980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 165 ASN B 703 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN D 957 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30444 Z= 0.182 Angle : 0.560 13.729 41396 Z= 0.290 Chirality : 0.044 0.212 4616 Planarity : 0.004 0.093 5375 Dihedral : 4.733 33.437 4050 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.73 % Allowed : 19.41 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3733 helix: 0.85 (0.17), residues: 1003 sheet: -0.35 (0.19), residues: 737 loop : -1.13 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.004 0.001 HIS A 374 PHE 0.022 0.001 PHE C 823 TYR 0.046 0.001 TYR B 707 ARG 0.008 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 314 time to evaluate : 3.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 331 average time/residue: 0.3998 time to fit residues: 220.5942 Evaluate side-chains 295 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 285 time to evaluate : 3.556 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2690 time to fit residues: 9.8180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 0.0970 chunk 348 optimal weight: 0.7980 chunk 317 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 305 optimal weight: 9.9990 chunk 320 optimal weight: 0.1980 chunk 337 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 703 ASN B 804 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 949 GLN C 969 ASN ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN D 245 HIS ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30444 Z= 0.171 Angle : 0.543 13.378 41396 Z= 0.280 Chirality : 0.043 0.249 4616 Planarity : 0.004 0.082 5375 Dihedral : 4.441 29.474 4050 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.51 % Allowed : 20.08 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3733 helix: 1.05 (0.17), residues: 1017 sheet: -0.25 (0.19), residues: 719 loop : -1.04 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 104 HIS 0.007 0.001 HIS D 245 PHE 0.022 0.001 PHE B 456 TYR 0.040 0.001 TYR A 41 ARG 0.006 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 316 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 324 average time/residue: 0.4112 time to fit residues: 224.6125 Evaluate side-chains 296 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 286 time to evaluate : 3.370 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3878 time to fit residues: 11.7937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 7.9990 chunk 358 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 248 optimal weight: 9.9990 chunk 375 optimal weight: 0.8980 chunk 345 optimal weight: 0.4980 chunk 299 optimal weight: 0.0000 chunk 31 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 99 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 30444 Z= 0.157 Angle : 0.533 13.090 41396 Z= 0.274 Chirality : 0.043 0.263 4616 Planarity : 0.004 0.077 5375 Dihedral : 4.255 26.775 4050 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.24 % Allowed : 20.41 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3733 helix: 1.13 (0.17), residues: 1015 sheet: -0.21 (0.19), residues: 723 loop : -0.95 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 104 HIS 0.004 0.001 HIS A 378 PHE 0.024 0.001 PHE C 823 TYR 0.038 0.001 TYR A 41 ARG 0.009 0.000 ARG D1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 302 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 305 average time/residue: 0.3884 time to fit residues: 201.5428 Evaluate side-chains 291 residues out of total 3302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 289 time to evaluate : 3.393 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3363 time to fit residues: 5.7524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 9.9990 chunk 318 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 275 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 307 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 969 ASN ** C1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.155657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.128291 restraints weight = 84500.655| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.05 r_work: 0.3816 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30444 Z= 0.162 Angle : 0.533 12.920 41396 Z= 0.273 Chirality : 0.043 0.268 4616 Planarity : 0.004 0.075 5375 Dihedral : 4.200 25.880 4050 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.18 % Allowed : 20.87 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3733 helix: 1.16 (0.17), residues: 1013 sheet: -0.19 (0.19), residues: 726 loop : -0.91 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 104 HIS 0.005 0.001 HIS A 374 PHE 0.022 0.001 PHE B 456 TYR 0.036 0.001 TYR A 41 ARG 0.008 0.000 ARG D1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7395.69 seconds wall clock time: 134 minutes 38.61 seconds (8078.61 seconds total)