Starting phenix.real_space_refine on Fri Mar 22 12:29:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo4_33336/03_2024/7xo4_33336.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo4_33336/03_2024/7xo4_33336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo4_33336/03_2024/7xo4_33336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo4_33336/03_2024/7xo4_33336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo4_33336/03_2024/7xo4_33336.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo4_33336/03_2024/7xo4_33336.pdb" } resolution = 3.24 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 161 5.16 5 C 21346 2.51 5 N 5518 2.21 5 O 6383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D ARG 577": "NH1" <-> "NH2" Residue "D ARG 600": "NH1" <-> "NH2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 312": "OE1" <-> "OE2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E ARG 387": "NH1" <-> "NH2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E GLU 489": "OE1" <-> "OE2" Residue "E TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 577": "NH1" <-> "NH2" Residue "E TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 600": "NH1" <-> "NH2" Residue "E TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33410 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7763 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 52, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "B" Number of atoms: 7763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7763 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 52, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "C" Number of atoms: 7700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7700 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 52, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 194 Chain: "D" Number of atoms: 4818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4818 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 25, 'TRANS': 565} Chain breaks: 1 Chain: "E" Number of atoms: 4818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4818 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 25, 'TRANS': 565} Chain breaks: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 16.95, per 1000 atoms: 0.51 Number of scatterers: 33410 At special positions: 0 Unit cell: (165.624, 140.08, 245.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 161 16.00 O 6383 8.00 N 5518 7.00 C 21346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.19 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.23 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.31 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=1.47 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.18 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=1.78 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=1.67 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.30 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 Links applied NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 331 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 343 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 603 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 370 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 801 " " NAG C1311 " - " ASN C 282 " " NAG D 902 " - " ASN D 546 " " NAG D 903 " - " ASN D 49 " " NAG E 902 " - " ASN E 546 " " NAG E 903 " - " ASN E 58 " Time building additional restraints: 12.47 Conformation dependent library (CDL) restraints added in 6.1 seconds 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8002 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 43 sheets defined 33.6% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.49 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.765A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.003A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.811A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.568A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.575A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.919A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.691A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.858A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.949A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.802A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 964 removed outlier: 4.556A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.739A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.569A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.584A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.563A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.014A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 749 through 754 removed outlier: 3.582A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 749 through 754' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.690A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.660A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.749A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.739A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.786A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.545A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.780A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.630A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.524A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.094A pdb=" N ASN C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.583A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.551A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.564A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 744 Processing helix chain 'C' and resid 753 through 757 removed outlier: 3.730A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.512A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.650A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.136A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.514A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.804A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.827A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 53 removed outlier: 3.947A pdb=" N LEU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 78 removed outlier: 3.633A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.700A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 removed outlier: 3.817A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 171 removed outlier: 3.672A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.923A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.829A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 199 through 204' Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.980A pdb=" N ASN D 216 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 248 removed outlier: 3.999A pdb=" N ASP D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.532A pdb=" N ALA D 242 " --> pdb=" O GLU D 238 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR D 243 " --> pdb=" O HIS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 298 removed outlier: 3.753A pdb=" N MET D 298 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 4.255A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.848A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 402 through 412 removed outlier: 3.800A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.554A pdb=" N LYS D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.565A pdb=" N GLN D 442 " --> pdb=" O PHE D 438 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.576A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.786A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 532 removed outlier: 4.064A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN D 522 " --> pdb=" O ARG D 518 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS D 530 " --> pdb=" O GLN D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.038A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER D 559 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.719A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 596 removed outlier: 3.889A pdb=" N LYS D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 53 removed outlier: 3.729A pdb=" N PHE E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP E 38 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 78 removed outlier: 3.706A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.668A pdb=" N SER E 82 " --> pdb=" O THR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 4.055A pdb=" N GLN E 96 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA E 99 " --> pdb=" O ARG E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.830A pdb=" N ASN E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 119 " --> pdb=" O GLN E 115 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 removed outlier: 3.710A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 174 removed outlier: 3.660A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP E 163 " --> pdb=" O ASN E 159 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 194 removed outlier: 3.929A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 205 removed outlier: 3.742A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 248 removed outlier: 3.683A pdb=" N GLU E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.447A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG E 245 " --> pdb=" O HIS E 241 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 247 " --> pdb=" O TYR E 243 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 295 through 300 removed outlier: 3.880A pdb=" N ASN E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 295 through 300' Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.836A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 329 removed outlier: 3.651A pdb=" N TRP E 328 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.712A pdb=" N GLY E 377 " --> pdb=" O HIS E 373 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 403 through 413 removed outlier: 4.101A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.657A pdb=" N GLY E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.571A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 448 No H-bonds generated for 'chain 'E' and resid 446 through 448' Processing helix chain 'E' and resid 449 through 465 removed outlier: 4.095A pdb=" N ARG E 465 " --> pdb=" O TRP E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 removed outlier: 4.003A pdb=" N ASN E 508 " --> pdb=" O PHE E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.094A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA E 533 " --> pdb=" O LEU E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.787A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS E 556 " --> pdb=" O GLN E 552 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.980A pdb=" N ASN E 572 " --> pdb=" O LYS E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.620A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.674A pdb=" N ASP E 593 " --> pdb=" O GLN E 589 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.747A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.656A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.977A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 310 through 319 removed outlier: 7.093A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.553A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.949A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.109A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.006A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.457A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.457A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.150A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.780A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.554A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.633A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 310 through 319 removed outlier: 5.295A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.621A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 43 " --> pdb=" O PHE B 565 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 376 through 380 removed outlier: 3.768A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.521A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.756A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 717 through 719 Processing sheet with id=AC7, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.546A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.047A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.733A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.345A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.833A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.291A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.742A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.019A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 362 removed outlier: 4.242A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.848A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.891A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C1070 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.891A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C1070 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.427A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.733A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 347 through 350 removed outlier: 4.046A pdb=" N THR D 347 " --> pdb=" O LYS D 359 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP D 349 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 350 through 352 removed outlier: 4.413A pdb=" N GLY E 352 " --> pdb=" O ASP E 355 " (cutoff:3.500A) 1234 hydrogen bonds defined for protein. 3483 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: 17.26 Time building geometry restraints manager: 13.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10666 1.34 - 1.46: 6608 1.46 - 1.58: 16721 1.58 - 1.70: 0 1.70 - 1.82: 225 Bond restraints: 34220 Sorted by residual: bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" N GLU E 145 " pdb=" CA GLU E 145 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.67e+00 bond pdb=" C1 NAG E 902 " pdb=" O5 NAG E 902 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" N LEU E 144 " pdb=" CA LEU E 144 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.64e+00 bond pdb=" C GLU E 145 " pdb=" N PRO E 146 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.19e-02 7.06e+03 5.64e+00 ... (remaining 34215 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.92: 1061 106.92 - 113.69: 18506 113.69 - 120.46: 13179 120.46 - 127.23: 13519 127.23 - 134.00: 371 Bond angle restraints: 46636 Sorted by residual: angle pdb=" N VAL A 503 " pdb=" CA VAL A 503 " pdb=" C VAL A 503 " ideal model delta sigma weight residual 113.71 108.98 4.73 9.50e-01 1.11e+00 2.48e+01 angle pdb=" C ASP E 149 " pdb=" N GLU E 150 " pdb=" CA GLU E 150 " ideal model delta sigma weight residual 120.60 113.96 6.64 1.60e+00 3.91e-01 1.72e+01 angle pdb=" N VAL E 574 " pdb=" CA VAL E 574 " pdb=" C VAL E 574 " ideal model delta sigma weight residual 113.53 109.84 3.69 9.80e-01 1.04e+00 1.42e+01 angle pdb=" N PRO A 373 " pdb=" CA PRO A 373 " pdb=" C PRO A 373 " ideal model delta sigma weight residual 114.68 110.18 4.50 1.28e+00 6.10e-01 1.24e+01 angle pdb=" N PHE A 375 " pdb=" CA PHE A 375 " pdb=" C PHE A 375 " ideal model delta sigma weight residual 113.18 109.03 4.15 1.21e+00 6.83e-01 1.18e+01 ... (remaining 46631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.13: 20116 23.13 - 46.25: 447 46.25 - 69.38: 72 69.38 - 92.50: 32 92.50 - 115.63: 46 Dihedral angle restraints: 20713 sinusoidal: 8298 harmonic: 12415 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 160.48 -67.48 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " pdb=" SG CYS D 542 " pdb=" CB CYS D 542 " ideal model delta sinusoidal sigma weight residual -86.00 -150.90 64.90 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 -141.35 55.35 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 20710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4804 0.069 - 0.137: 515 0.137 - 0.206: 7 0.206 - 0.275: 4 0.275 - 0.343: 5 Chirality restraints: 5335 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 5332 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 986 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 987 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 234 " 0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO D 235 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " 0.020 5.00e-02 4.00e+02 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.93: 4 1.93 - 2.67: 468 2.67 - 3.41: 44450 3.41 - 4.16: 75159 4.16 - 4.90: 135515 Nonbonded interactions: 255596 Sorted by model distance: nonbonded pdb=" NE2 GLN E 388 " pdb=" O LEU E 392 " model vdw 1.184 2.520 nonbonded pdb=" CG1 VAL A1094 " pdb=" OH TYR B 904 " model vdw 1.688 3.460 nonbonded pdb=" OE1 GLU C 406 " pdb=" OE1 GLN C 409 " model vdw 1.877 3.040 nonbonded pdb=" OE1 GLU C 406 " pdb=" CD GLN C 409 " model vdw 1.925 3.270 nonbonded pdb=" OE1 GLU C 406 " pdb=" NE2 GLN C 409 " model vdw 1.947 2.520 ... (remaining 255591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 68 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 86 or (resid 87 and (name N or name CA or name C or n \ ame O or name CB )) or resid 88 through 96 or (resid 97 through 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 114 or (resid 11 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 116 through \ 133 or (resid 134 and (name N or name CA or name C or name O or name CB )) or re \ sid 135 through 136 or (resid 137 and (name N or name CA or name C or name O or \ name CB )) or resid 138 through 160 or (resid 161 through 164 and (name N or nam \ e CA or name C or name O or name CB )) or resid 165 through 209 or (resid 210 an \ d (name N or name CA or name C or name O or name CB )) or resid 215 through 253 \ or (resid 254 and (name N or name CA or name C or name O or name CB )) or resid \ 255 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 355 or (resid 356 through 357 and (name N or name CA \ or name C or name O or name CB )) or resid 358 through 387 or (resid 388 and (n \ ame N or name CA or name C or name O or name CB )) or resid 389 through 404 or ( \ resid 405 and (name N or name CA or name C or name O or name CB )) or resid 406 \ through 414 or (resid 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 through 426 or (resid 427 and (name N or name CA or name C or na \ me O or name CB )) or resid 428 through 447 or (resid 448 and (name N or name CA \ or name C or name O or name CB )) or resid 449 through 453 or (resid 454 and (n \ ame N or name CA or name C or name O or name CB )) or resid 455 through 457 or ( \ resid 458 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 464 or (resid 465 and (name N or name CA or name C or name O \ or name CB )) or resid 466 through 473 or (resid 474 through 475 and (name N or \ name CA or name C or name O or name CB )) or resid 476 through 486 or (resid 48 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 488 through \ 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) or re \ sid 501 through 515 or (resid 516 and (name N or name CA or name C or name O or \ name CB )) or resid 517 through 522 or (resid 523 and (name N or name CA or name \ C or name O or name CB )) or resid 524 through 527 or (resid 528 through 529 an \ d (name N or name CA or name C or name O or name CB )) or resid 530 through 553 \ or (resid 554 and (name N or name CA or name C or name O or name CB )) or resid \ 555 or (resid 556 through 558 and (name N or name CA or name C or name O or name \ CB )) or resid 559 through 563 or (resid 564 and (name N or name CA or name C o \ r name O or name CB )) or resid 565 through 570 or (resid 571 through 572 and (n \ ame N or name CA or name C or name O or name CB )) or resid 573 through 620 or r \ esid 641 through 676 or (resid 690 and (name N or name CA or name C or name O or \ name CB )) or resid 691 through 747 or (resid 748 and (name N or name CA or nam \ e C or name O or name CB )) or resid 749 through 827 or (resid 828 and (name N o \ r name CA or name C or name O or name CB )) or resid 855 through 984 or (resid 9 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 986 through \ 987 or (resid 988 through 989 and (name N or name CA or name C or name O or nam \ e CB )) or resid 990 through 1037 or (resid 1038 and (name N or name CA or name \ C or name O or name CB )) or resid 1039 through 1050 or (resid 1051 and (name N \ or name CA or name C or name O or name CB )) or resid 1052 through 1110 or (resi \ d 1111 and (name N or name CA or name C or name O or name CB )) or resid 1112 th \ rough 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name \ O or name CB )) or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 68 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 86 or (resid 87 and (name N or name CA or name C or n \ ame O or name CB )) or resid 88 through 96 or (resid 97 through 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 114 or (resid 11 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 116 through \ 133 or (resid 134 and (name N or name CA or name C or name O or name CB )) or re \ sid 135 through 136 or (resid 137 and (name N or name CA or name C or name O or \ name CB )) or resid 138 through 160 or (resid 161 through 164 and (name N or nam \ e CA or name C or name O or name CB )) or resid 165 through 209 or (resid 210 an \ d (name N or name CA or name C or name O or name CB )) or resid 215 through 253 \ or (resid 254 and (name N or name CA or name C or name O or name CB )) or resid \ 255 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 355 or (resid 356 through 357 and (name N or name CA \ or name C or name O or name CB )) or resid 358 through 387 or (resid 388 and (n \ ame N or name CA or name C or name O or name CB )) or resid 389 through 404 or ( \ resid 405 and (name N or name CA or name C or name O or name CB )) or resid 406 \ through 414 or (resid 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 through 426 or (resid 427 and (name N or name CA or name C or na \ me O or name CB )) or resid 428 through 447 or (resid 448 and (name N or name CA \ or name C or name O or name CB )) or resid 449 through 453 or (resid 454 and (n \ ame N or name CA or name C or name O or name CB )) or resid 455 through 457 or ( \ resid 458 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 464 or (resid 465 and (name N or name CA or name C or name O \ or name CB )) or resid 466 through 473 or (resid 474 through 475 and (name N or \ name CA or name C or name O or name CB )) or resid 476 through 486 or (resid 48 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 488 through \ 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) or re \ sid 501 through 515 or (resid 516 and (name N or name CA or name C or name O or \ name CB )) or resid 517 through 522 or (resid 523 and (name N or name CA or name \ C or name O or name CB )) or resid 524 through 527 or (resid 528 through 529 an \ d (name N or name CA or name C or name O or name CB )) or resid 530 through 553 \ or (resid 554 and (name N or name CA or name C or name O or name CB )) or resid \ 555 or (resid 556 through 558 and (name N or name CA or name C or name O or name \ CB )) or resid 559 through 563 or (resid 564 and (name N or name CA or name C o \ r name O or name CB )) or resid 565 through 570 or (resid 571 through 572 and (n \ ame N or name CA or name C or name O or name CB )) or resid 573 through 620 or r \ esid 641 through 676 or (resid 690 and (name N or name CA or name C or name O or \ name CB )) or resid 691 through 747 or (resid 748 and (name N or name CA or nam \ e C or name O or name CB )) or resid 749 through 827 or (resid 828 and (name N o \ r name CA or name C or name O or name CB )) or resid 855 through 984 or (resid 9 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 986 through \ 987 or (resid 988 through 989 and (name N or name CA or name C or name O or nam \ e CB )) or resid 990 through 1037 or (resid 1038 and (name N or name CA or name \ C or name O or name CB )) or resid 1039 through 1050 or (resid 1051 and (name N \ or name CA or name C or name O or name CB )) or resid 1052 through 1110 or (resi \ d 1111 and (name N or name CA or name C or name O or name CB )) or resid 1112 th \ rough 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name \ O or name CB )) or resid 1301 through 1311)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 67 or (resid 68 through 80 and (na \ me N or name CA or name C or name O or name CB )) or resid 81 through 107 or (re \ sid 108 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 175 or (resid 176 through 187 and (name N or name CA or name C \ or name O or name CB )) or resid 188 through 199 or (resid 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 22 \ 3 or (resid 224 and (name N or name CA or name C or name O or name CB )) or resi \ d 225 through 248 or (resid 249 through 250 and (name N or name CA or name C or \ name O or name CB )) or resid 251 through 303 or (resid 304 and (name N or name \ CA or name C or name O or name CB )) or resid 305 through 320 or (resid 321 and \ (name N or name CA or name C or name O or name CB )) or resid 322 through 556 or \ (resid 557 through 558 and (name N or name CA or name C or name O or name CB )) \ or resid 559 through 568 or (resid 569 through 572 and (name N or name CA or na \ me C or name O or name CB )) or resid 573 through 662 or (resid 663 and (name N \ or name CA or name C or name O or name CB )) or resid 664 through 701 or (resid \ 702 and (name N or name CA or name C or name O or name CB )) or resid 703 throug \ h 739 or (resid 740 and (name N or name CA or name C or name O or name CB )) or \ resid 741 through 794 or (resid 795 and (name N or name CA or name C or name O o \ r name CB )) or resid 796 through 807 or (resid 808 and (name N or name CA or na \ me C or name O or name CB )) or resid 809 through 818 or (resid 819 and (name N \ or name CA or name C or name O or name CB )) or resid 820 through 824 or (resid \ 825 and (name N or name CA or name C or name O or name CB )) or resid 826 throug \ h 917 or (resid 918 and (name N or name CA or name C or name O or name CB )) or \ resid 919 through 946 or (resid 947 and (name N or name CA or name C or name O o \ r name CB )) or resid 948 through 963 or (resid 964 and (name N or name CA or na \ me C or name O or name CB )) or resid 965 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1137 or (re \ sid 1138 and (name N or name CA or name C or name O or name CB )) or resid 1139 \ through 1140 or (resid 1141 through 1142 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1143 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O or name CB )) or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 11.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 24.190 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 89.720 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.190 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3835 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 : 0.002 0.080 34220 Z= 0.157 Angle : 0.504 6.637 46636 Z= 0.289 Chirality : 0.042 0.343 5335 Planarity : 0.003 0.036 5997 Dihedral : 11.874 115.631 12600 Min Nonbonded Distance : 1.184 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.11), residues: 4196 helix: -1.35 (0.13), residues: 1207 sheet: -1.06 (0.18), residues: 699 loop : -2.51 (0.11), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 594 HIS 0.003 0.000 HIS E 265 PHE 0.009 0.001 PHE A 168 TYR 0.009 0.001 TYR A 495 ARG 0.002 0.000 ARG E 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 605 time to evaluate : 3.394 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: A 53 ASP cc_start: 0.6621 (t0) cc_final: 0.6379 (t0) REVERT: A 238 PHE cc_start: 0.6843 (p90) cc_final: 0.6358 (p90) REVERT: A 266 TYR cc_start: 0.7058 (m-80) cc_final: 0.6852 (m-80) REVERT: A 743 CYS cc_start: 0.5933 (m) cc_final: 0.5686 (m) REVERT: A 776 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7607 (ttpt) REVERT: A 779 GLN cc_start: 0.8121 (tt0) cc_final: 0.7862 (tt0) REVERT: A 881 THR cc_start: 0.7957 (m) cc_final: 0.7411 (p) REVERT: A 1038 LYS cc_start: 0.7317 (mtpp) cc_final: 0.7116 (mtpp) REVERT: A 1116 THR cc_start: 0.7295 (p) cc_final: 0.7077 (m) REVERT: B 309 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6598 (mt-10) REVERT: B 605 SER cc_start: 0.7595 (t) cc_final: 0.7289 (t) REVERT: B 730 SER cc_start: 0.7953 (p) cc_final: 0.7663 (t) REVERT: B 1127 ASP cc_start: 0.7276 (t70) cc_final: 0.6982 (t0) REVERT: C 543 PHE cc_start: 0.7175 (m-10) cc_final: 0.6945 (m-80) REVERT: C 902 MET cc_start: 0.8232 (mmt) cc_final: 0.8027 (mmt) REVERT: C 964 LYS cc_start: 0.7534 (tttp) cc_final: 0.7322 (ttmm) REVERT: D 270 MET cc_start: -0.0438 (mtt) cc_final: -0.3977 (ttt) REVERT: D 332 MET cc_start: -0.0530 (ttm) cc_final: -0.0937 (ttm) REVERT: D 366 MET cc_start: 0.0929 (ttt) cc_final: 0.0671 (ttt) REVERT: E 360 MET cc_start: -0.0386 (ttt) cc_final: -0.0593 (tpt) outliers start: 0 outliers final: 0 residues processed: 605 average time/residue: 0.4018 time to fit residues: 401.8326 Evaluate side-chains 481 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 8.9990 chunk 321 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 332 optimal weight: 30.0000 chunk 128 optimal weight: 0.9990 chunk 202 optimal weight: 0.0970 chunk 247 optimal weight: 0.1980 chunk 385 optimal weight: 50.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 207 HIS A 271 GLN A 422 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN A 774 GLN A 920 GLN A 926 GLN A 965 GLN A1071 GLN A1134 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 314 GLN B 394 ASN B 448 ASN B 474 GLN B 644 GLN B 690 GLN B 755 GLN B 914 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 978 ASN B1023 ASN B1135 ASN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 710 ASN C 777 ASN C 784 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 920 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN D 42 GLN D 89 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN D 115 GLN D 159 ASN D 353 HIS D 397 ASN D 524 GLN D 540 HIS ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 101 GLN E 102 GLN E 221 GLN E 277 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN E 368 ASN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 HIS ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 GLN E 531 GLN ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4129 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 34220 Z= 0.246 Angle : 0.593 11.085 46636 Z= 0.289 Chirality : 0.047 0.559 5335 Planarity : 0.004 0.054 5997 Dihedral : 8.220 103.619 5368 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.27 % Allowed : 9.91 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.12), residues: 4196 helix: -0.14 (0.15), residues: 1234 sheet: -0.83 (0.17), residues: 791 loop : -2.09 (0.12), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 477 HIS 0.010 0.001 HIS A1064 PHE 0.023 0.002 PHE C 55 TYR 0.024 0.002 TYR C 265 ARG 0.006 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 549 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6295 (p) cc_final: 0.5362 (t) REVERT: A 170 TYR cc_start: 0.6867 (t80) cc_final: 0.6647 (t80) REVERT: A 266 TYR cc_start: 0.7150 (m-80) cc_final: 0.6900 (m-80) REVERT: A 643 PHE cc_start: 0.7917 (t80) cc_final: 0.7710 (t80) REVERT: A 691 SER cc_start: 0.8088 (OUTLIER) cc_final: 0.7885 (t) REVERT: A 784 GLN cc_start: 0.7771 (mt0) cc_final: 0.7566 (mt0) REVERT: A 881 THR cc_start: 0.8266 (m) cc_final: 0.7430 (p) REVERT: A 955 ASN cc_start: 0.7640 (t0) cc_final: 0.7426 (t0) REVERT: A 1072 GLU cc_start: 0.7455 (pm20) cc_final: 0.7249 (pm20) REVERT: B 204 TYR cc_start: 0.7575 (m-10) cc_final: 0.7154 (m-80) REVERT: B 320 VAL cc_start: 0.8542 (t) cc_final: 0.8312 (t) REVERT: B 642 VAL cc_start: 0.8714 (t) cc_final: 0.8484 (p) REVERT: B 658 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7394 (p0) REVERT: B 696 THR cc_start: 0.7456 (p) cc_final: 0.6896 (t) REVERT: B 776 LYS cc_start: 0.7712 (ttmm) cc_final: 0.7480 (ttmm) REVERT: B 873 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: B 878 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7922 (mt) REVERT: B 1122 VAL cc_start: 0.8190 (t) cc_final: 0.7975 (m) REVERT: C 195 LYS cc_start: 0.7539 (ptmt) cc_final: 0.7295 (ptmt) REVERT: C 273 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7472 (mmm160) REVERT: C 281 GLU cc_start: 0.6091 (pp20) cc_final: 0.5879 (pp20) REVERT: C 396 TYR cc_start: 0.6424 (m-80) cc_final: 0.6182 (m-80) REVERT: C 436 TRP cc_start: 0.7244 (p90) cc_final: 0.6952 (p90) REVERT: C 596 SER cc_start: 0.8103 (t) cc_final: 0.7887 (p) REVERT: C 705 VAL cc_start: 0.6392 (OUTLIER) cc_final: 0.4844 (m) REVERT: C 814 LYS cc_start: 0.8250 (mptt) cc_final: 0.7963 (mmtm) REVERT: C 1019 ARG cc_start: 0.7249 (tpt170) cc_final: 0.7047 (tpt170) REVERT: C 1066 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7756 (p) REVERT: C 1092 GLU cc_start: 0.6860 (mp0) cc_final: 0.6659 (mp0) REVERT: D 270 MET cc_start: -0.0316 (mtt) cc_final: -0.3816 (ttt) REVERT: D 332 MET cc_start: -0.0666 (ttm) cc_final: -0.1048 (ttm) REVERT: E 360 MET cc_start: -0.0157 (ttt) cc_final: -0.0399 (tpt) REVERT: E 366 MET cc_start: 0.3314 (tpp) cc_final: 0.2975 (mmt) outliers start: 79 outliers final: 36 residues processed: 603 average time/residue: 0.4111 time to fit residues: 410.3911 Evaluate side-chains 530 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 488 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain E residue 221 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 320 optimal weight: 20.0000 chunk 262 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 385 optimal weight: 9.9990 chunk 416 optimal weight: 0.7980 chunk 343 optimal weight: 40.0000 chunk 382 optimal weight: 10.0000 chunk 131 optimal weight: 40.0000 chunk 309 optimal weight: 9.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 774 GLN A 824 ASN A 955 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 913 GLN B 925 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1083 HIS C1101 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN E 96 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4408 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.163 34220 Z= 0.812 Angle : 0.846 18.099 46636 Z= 0.433 Chirality : 0.060 0.525 5335 Planarity : 0.006 0.092 5997 Dihedral : 7.630 90.020 5368 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.65 % Allowed : 11.87 % Favored : 84.48 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.84 (0.12), residues: 4196 helix: -0.08 (0.14), residues: 1231 sheet: -0.91 (0.17), residues: 805 loop : -2.06 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.022 0.002 HIS C1064 PHE 0.045 0.004 PHE A 906 TYR 0.053 0.003 TYR C 265 ARG 0.008 0.001 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 600 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.7993 (OUTLIER) cc_final: 0.7788 (p) REVERT: A 66 HIS cc_start: 0.6689 (m90) cc_final: 0.6425 (m90) REVERT: A 127 VAL cc_start: 0.7990 (t) cc_final: 0.7680 (m) REVERT: A 294 ASP cc_start: 0.6906 (p0) cc_final: 0.6598 (p0) REVERT: A 307 THR cc_start: 0.8500 (m) cc_final: 0.8145 (p) REVERT: A 532 ASN cc_start: 0.6054 (OUTLIER) cc_final: 0.5002 (p0) REVERT: A 571 ASP cc_start: 0.6251 (t0) cc_final: 0.5878 (t0) REVERT: A 722 VAL cc_start: 0.8716 (m) cc_final: 0.8366 (t) REVERT: A 748 GLU cc_start: 0.6776 (mp0) cc_final: 0.6474 (mp0) REVERT: A 811 LYS cc_start: 0.8047 (mmtp) cc_final: 0.7778 (mttm) REVERT: A 820 ASP cc_start: 0.7259 (m-30) cc_final: 0.6970 (m-30) REVERT: A 872 GLN cc_start: 0.7842 (tt0) cc_final: 0.7616 (mt0) REVERT: A 1097 SER cc_start: 0.8720 (t) cc_final: 0.8397 (p) REVERT: A 1125 ASN cc_start: 0.7770 (p0) cc_final: 0.7522 (p0) REVERT: A 1127 ASP cc_start: 0.7517 (p0) cc_final: 0.6904 (p0) REVERT: B 40 ASP cc_start: 0.6914 (p0) cc_final: 0.6509 (p0) REVERT: B 42 VAL cc_start: 0.7886 (t) cc_final: 0.7543 (p) REVERT: B 318 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8150 (p90) REVERT: B 549 THR cc_start: 0.8211 (m) cc_final: 0.7895 (p) REVERT: B 708 SER cc_start: 0.7774 (t) cc_final: 0.7509 (p) REVERT: B 710 ASN cc_start: 0.8094 (p0) cc_final: 0.7795 (p0) REVERT: B 776 LYS cc_start: 0.7840 (ttmm) cc_final: 0.7618 (ttmm) REVERT: B 804 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7427 (mm-40) REVERT: B 826 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7835 (p) REVERT: B 935 GLN cc_start: 0.7514 (mt0) cc_final: 0.7141 (mt0) REVERT: B 969 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8239 (mtmm) REVERT: B 996 LEU cc_start: 0.8159 (mp) cc_final: 0.7941 (mt) REVERT: B 1031 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7555 (mt-10) REVERT: B 1118 ASP cc_start: 0.7495 (p0) cc_final: 0.7207 (p0) REVERT: B 1122 VAL cc_start: 0.8376 (t) cc_final: 0.8128 (m) REVERT: C 51 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8005 (p) REVERT: C 321 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7722 (mm-40) REVERT: C 351 TYR cc_start: 0.7832 (p90) cc_final: 0.7436 (p90) REVERT: C 355 ARG cc_start: 0.7622 (mtp180) cc_final: 0.7207 (mmm160) REVERT: C 365 TYR cc_start: 0.7947 (m-80) cc_final: 0.7727 (m-80) REVERT: C 385 THR cc_start: 0.8506 (m) cc_final: 0.8274 (t) REVERT: C 396 TYR cc_start: 0.7130 (m-80) cc_final: 0.6713 (m-10) REVERT: C 400 PHE cc_start: 0.7392 (p90) cc_final: 0.6831 (p90) REVERT: C 436 TRP cc_start: 0.7390 (p90) cc_final: 0.7141 (p90) REVERT: C 440 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8678 (ttpp) REVERT: C 603 ASN cc_start: 0.6893 (t0) cc_final: 0.6572 (t0) REVERT: C 644 GLN cc_start: 0.7847 (tp40) cc_final: 0.7546 (tp40) REVERT: C 670 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8121 (pt) REVERT: C 722 VAL cc_start: 0.8823 (m) cc_final: 0.8569 (t) REVERT: C 772 VAL cc_start: 0.8551 (t) cc_final: 0.8168 (m) REVERT: C 784 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: C 814 LYS cc_start: 0.8316 (mptt) cc_final: 0.8066 (mmtm) REVERT: C 949 GLN cc_start: 0.7781 (tp-100) cc_final: 0.7579 (tp-100) REVERT: C 995 ARG cc_start: 0.7641 (ttm170) cc_final: 0.7426 (ttm110) REVERT: C 997 ILE cc_start: 0.8545 (mm) cc_final: 0.8316 (mt) REVERT: C 1037 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7970 (p) REVERT: C 1130 ILE cc_start: 0.8676 (mt) cc_final: 0.8475 (mt) REVERT: D 332 MET cc_start: -0.0690 (ttm) cc_final: -0.0998 (ttm) REVERT: E 360 MET cc_start: -0.0054 (ttt) cc_final: -0.0433 (tpt) outliers start: 127 outliers final: 64 residues processed: 682 average time/residue: 0.4122 time to fit residues: 466.4856 Evaluate side-chains 622 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 550 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 7.9990 chunk 290 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 42 optimal weight: 0.0010 chunk 184 optimal weight: 0.5980 chunk 259 optimal weight: 0.6980 chunk 387 optimal weight: 20.0000 chunk 409 optimal weight: 10.0000 chunk 202 optimal weight: 0.5980 chunk 366 optimal weight: 5.9990 chunk 110 optimal weight: 0.3980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 762 GLN B 784 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 271 GLN C 613 GLN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4308 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34220 Z= 0.184 Angle : 0.564 11.632 46636 Z= 0.279 Chirality : 0.045 0.410 5335 Planarity : 0.004 0.051 5997 Dihedral : 6.662 90.379 5368 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.70 % Allowed : 14.63 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4196 helix: 0.55 (0.15), residues: 1227 sheet: -0.65 (0.17), residues: 821 loop : -1.82 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.004 0.001 HIS C1064 PHE 0.031 0.001 PHE B 329 TYR 0.026 0.001 TYR A 170 ARG 0.005 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 554 time to evaluate : 3.873 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: A 168 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.5626 (p90) REVERT: A 294 ASP cc_start: 0.6823 (p0) cc_final: 0.6560 (p0) REVERT: A 571 ASP cc_start: 0.6182 (t0) cc_final: 0.5833 (t0) REVERT: A 722 VAL cc_start: 0.8637 (m) cc_final: 0.8321 (t) REVERT: A 773 GLU cc_start: 0.6589 (tt0) cc_final: 0.6383 (tt0) REVERT: A 778 THR cc_start: 0.8917 (t) cc_final: 0.8649 (m) REVERT: A 811 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7775 (mttm) REVERT: A 820 ASP cc_start: 0.7119 (m-30) cc_final: 0.6824 (m-30) REVERT: A 872 GLN cc_start: 0.7653 (tt0) cc_final: 0.7428 (mt0) REVERT: A 970 PHE cc_start: 0.8450 (m-80) cc_final: 0.8249 (m-10) REVERT: A 1127 ASP cc_start: 0.7483 (p0) cc_final: 0.6607 (p0) REVERT: A 1139 ASP cc_start: 0.7471 (t0) cc_final: 0.7181 (t0) REVERT: B 42 VAL cc_start: 0.7742 (t) cc_final: 0.7514 (t) REVERT: B 318 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8167 (p90) REVERT: B 549 THR cc_start: 0.8068 (m) cc_final: 0.7647 (p) REVERT: B 703 ASN cc_start: 0.7751 (t0) cc_final: 0.7509 (t0) REVERT: B 708 SER cc_start: 0.7699 (t) cc_final: 0.7417 (m) REVERT: B 710 ASN cc_start: 0.7976 (p0) cc_final: 0.7688 (p0) REVERT: B 826 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7577 (p) REVERT: B 949 GLN cc_start: 0.7901 (tp40) cc_final: 0.7539 (tp40) REVERT: B 969 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8089 (mtmm) REVERT: B 1029 MET cc_start: 0.8118 (tpp) cc_final: 0.7840 (ttm) REVERT: B 1118 ASP cc_start: 0.7332 (p0) cc_final: 0.7067 (p0) REVERT: B 1122 VAL cc_start: 0.8304 (t) cc_final: 0.8074 (m) REVERT: C 51 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8038 (p) REVERT: C 90 VAL cc_start: 0.8093 (t) cc_final: 0.7804 (p) REVERT: C 351 TYR cc_start: 0.7802 (p90) cc_final: 0.7239 (p90) REVERT: C 355 ARG cc_start: 0.7435 (mtp180) cc_final: 0.7185 (mmm160) REVERT: C 365 TYR cc_start: 0.7837 (m-80) cc_final: 0.7581 (m-80) REVERT: C 385 THR cc_start: 0.8444 (m) cc_final: 0.8202 (t) REVERT: C 396 TYR cc_start: 0.7064 (m-80) cc_final: 0.6798 (m-10) REVERT: C 400 PHE cc_start: 0.7389 (p90) cc_final: 0.6830 (p90) REVERT: C 436 TRP cc_start: 0.7425 (p90) cc_final: 0.7102 (p90) REVERT: C 581 THR cc_start: 0.7881 (t) cc_final: 0.7429 (t) REVERT: C 603 ASN cc_start: 0.6749 (t0) cc_final: 0.6434 (t0) REVERT: C 608 VAL cc_start: 0.8619 (t) cc_final: 0.8212 (p) REVERT: C 670 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8062 (pt) REVERT: C 772 VAL cc_start: 0.8385 (t) cc_final: 0.8123 (m) REVERT: C 784 GLN cc_start: 0.8243 (mt0) cc_final: 0.8021 (mm-40) REVERT: C 814 LYS cc_start: 0.8265 (mptt) cc_final: 0.8003 (mmtm) REVERT: C 825 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7934 (ttpp) REVERT: C 884 SER cc_start: 0.8654 (m) cc_final: 0.8416 (m) REVERT: C 949 GLN cc_start: 0.7513 (tp-100) cc_final: 0.7275 (tp-100) REVERT: C 997 ILE cc_start: 0.8458 (mm) cc_final: 0.8187 (mt) REVERT: C 1037 SER cc_start: 0.8197 (t) cc_final: 0.7880 (p) REVERT: D 332 MET cc_start: -0.0793 (ttm) cc_final: -0.1209 (ttm) REVERT: E 360 MET cc_start: 0.0034 (ttt) cc_final: -0.0175 (tpt) REVERT: E 366 MET cc_start: 0.3209 (tpt) cc_final: 0.2767 (mmt) outliers start: 94 outliers final: 54 residues processed: 616 average time/residue: 0.4192 time to fit residues: 431.8831 Evaluate side-chains 577 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 518 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 50.0000 chunk 232 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 349 optimal weight: 3.9990 chunk 283 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 367 optimal weight: 50.0000 chunk 103 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 762 GLN B 784 GLN B 901 GLN B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 613 GLN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1002 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4370 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 34220 Z= 0.404 Angle : 0.622 14.778 46636 Z= 0.311 Chirality : 0.048 0.535 5335 Planarity : 0.005 0.064 5997 Dihedral : 6.475 90.204 5368 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.33 % Allowed : 15.52 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.22 (0.12), residues: 4196 helix: 0.63 (0.15), residues: 1234 sheet: -0.61 (0.17), residues: 837 loop : -1.80 (0.12), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.009 0.001 HIS A1064 PHE 0.030 0.002 PHE C 168 TYR 0.029 0.002 TYR A 170 ARG 0.005 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 526 time to evaluate : 3.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8018 (m) cc_final: 0.7768 (p) REVERT: A 168 PHE cc_start: 0.6503 (OUTLIER) cc_final: 0.6127 (p90) REVERT: A 294 ASP cc_start: 0.6831 (p0) cc_final: 0.6557 (p0) REVERT: A 543 PHE cc_start: 0.7528 (m-10) cc_final: 0.7324 (m-10) REVERT: A 571 ASP cc_start: 0.6379 (t0) cc_final: 0.6027 (t0) REVERT: A 722 VAL cc_start: 0.8586 (m) cc_final: 0.8252 (t) REVERT: A 872 GLN cc_start: 0.7745 (tt0) cc_final: 0.7527 (mt0) REVERT: A 1120 THR cc_start: 0.8475 (m) cc_final: 0.8271 (p) REVERT: A 1125 ASN cc_start: 0.7586 (p0) cc_final: 0.7315 (p0) REVERT: A 1127 ASP cc_start: 0.7377 (p0) cc_final: 0.6920 (p0) REVERT: B 48 LEU cc_start: 0.8261 (mt) cc_final: 0.7914 (mt) REVERT: B 50 SER cc_start: 0.8537 (m) cc_final: 0.8136 (p) REVERT: B 318 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.8207 (p90) REVERT: B 549 THR cc_start: 0.8144 (m) cc_final: 0.7776 (p) REVERT: B 708 SER cc_start: 0.7749 (t) cc_final: 0.7452 (m) REVERT: B 710 ASN cc_start: 0.8141 (p0) cc_final: 0.7799 (p0) REVERT: B 949 GLN cc_start: 0.7934 (tp40) cc_final: 0.7557 (tp-100) REVERT: B 969 LYS cc_start: 0.8352 (mtmt) cc_final: 0.8088 (mtmm) REVERT: B 1029 MET cc_start: 0.8182 (tpp) cc_final: 0.7897 (ttm) REVERT: C 51 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8005 (p) REVERT: C 90 VAL cc_start: 0.8142 (t) cc_final: 0.7880 (p) REVERT: C 342 PHE cc_start: 0.8431 (m-80) cc_final: 0.8018 (t80) REVERT: C 351 TYR cc_start: 0.7947 (p90) cc_final: 0.7314 (p90) REVERT: C 355 ARG cc_start: 0.7510 (mtp180) cc_final: 0.7159 (mmm160) REVERT: C 365 TYR cc_start: 0.7884 (m-80) cc_final: 0.7682 (m-80) REVERT: C 385 THR cc_start: 0.8619 (m) cc_final: 0.8403 (t) REVERT: C 396 TYR cc_start: 0.7274 (m-80) cc_final: 0.6896 (m-10) REVERT: C 400 PHE cc_start: 0.7405 (p90) cc_final: 0.6885 (p90) REVERT: C 538 CYS cc_start: 0.5511 (t) cc_final: 0.5139 (t) REVERT: C 603 ASN cc_start: 0.6763 (t0) cc_final: 0.6483 (t0) REVERT: C 608 VAL cc_start: 0.8662 (t) cc_final: 0.8236 (p) REVERT: C 644 GLN cc_start: 0.7783 (tp40) cc_final: 0.7476 (tp40) REVERT: C 670 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8115 (pt) REVERT: C 722 VAL cc_start: 0.8845 (m) cc_final: 0.8613 (t) REVERT: C 784 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: C 825 LYS cc_start: 0.8262 (ttpp) cc_final: 0.8018 (ttpp) REVERT: C 949 GLN cc_start: 0.7645 (tp-100) cc_final: 0.7418 (tp-100) REVERT: C 1037 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7883 (p) REVERT: D 332 MET cc_start: -0.0850 (ttm) cc_final: -0.1330 (ttm) REVERT: E 360 MET cc_start: 0.0065 (ttt) cc_final: -0.0258 (tpt) REVERT: E 366 MET cc_start: 0.3240 (tpt) cc_final: 0.1675 (tpt) REVERT: E 544 ILE cc_start: -0.0228 (OUTLIER) cc_final: -0.0599 (mm) outliers start: 116 outliers final: 80 residues processed: 598 average time/residue: 0.4189 time to fit residues: 415.0437 Evaluate side-chains 609 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 522 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 7.9990 chunk 369 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 410 optimal weight: 8.9990 chunk 340 optimal weight: 50.0000 chunk 189 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 135 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 762 GLN B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN E 221 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4367 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 34220 Z= 0.337 Angle : 0.595 14.618 46636 Z= 0.297 Chirality : 0.047 0.483 5335 Planarity : 0.004 0.052 5997 Dihedral : 6.249 88.819 5368 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.71 % Allowed : 15.98 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.04 (0.12), residues: 4196 helix: 0.87 (0.15), residues: 1226 sheet: -0.54 (0.17), residues: 827 loop : -1.73 (0.12), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 436 HIS 0.008 0.001 HIS A1064 PHE 0.027 0.002 PHE C 168 TYR 0.028 0.001 TYR A 170 ARG 0.006 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 552 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8041 (m) cc_final: 0.7788 (p) REVERT: A 63 THR cc_start: 0.7246 (p) cc_final: 0.6330 (t) REVERT: A 204 TYR cc_start: 0.8457 (m-80) cc_final: 0.8189 (m-80) REVERT: A 216 LEU cc_start: 0.7023 (mt) cc_final: 0.6792 (mt) REVERT: A 294 ASP cc_start: 0.6794 (p0) cc_final: 0.6530 (p0) REVERT: A 543 PHE cc_start: 0.7490 (m-10) cc_final: 0.7270 (m-10) REVERT: A 571 ASP cc_start: 0.6484 (t0) cc_final: 0.6118 (t0) REVERT: A 748 GLU cc_start: 0.6716 (mp0) cc_final: 0.6392 (mp0) REVERT: A 778 THR cc_start: 0.8869 (t) cc_final: 0.8629 (m) REVERT: A 872 GLN cc_start: 0.7749 (tt0) cc_final: 0.7524 (mt0) REVERT: A 968 SER cc_start: 0.8370 (m) cc_final: 0.8026 (t) REVERT: A 1120 THR cc_start: 0.8438 (m) cc_final: 0.8235 (p) REVERT: B 48 LEU cc_start: 0.8325 (mt) cc_final: 0.8095 (mp) REVERT: B 50 SER cc_start: 0.8511 (m) cc_final: 0.8111 (p) REVERT: B 318 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8160 (p90) REVERT: B 549 THR cc_start: 0.8130 (m) cc_final: 0.7818 (p) REVERT: B 704 SER cc_start: 0.8281 (t) cc_final: 0.7956 (p) REVERT: B 708 SER cc_start: 0.7749 (t) cc_final: 0.7481 (m) REVERT: B 710 ASN cc_start: 0.8127 (p0) cc_final: 0.7779 (p0) REVERT: B 957 GLN cc_start: 0.7037 (tm-30) cc_final: 0.6697 (tm-30) REVERT: B 969 LYS cc_start: 0.8317 (mtmt) cc_final: 0.8063 (mtmm) REVERT: B 1029 MET cc_start: 0.8210 (tpp) cc_final: 0.7908 (ttm) REVERT: B 1118 ASP cc_start: 0.7367 (p0) cc_final: 0.7156 (p0) REVERT: C 51 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7990 (p) REVERT: C 90 VAL cc_start: 0.8118 (t) cc_final: 0.7832 (p) REVERT: C 165 ASN cc_start: 0.3782 (OUTLIER) cc_final: 0.3452 (t0) REVERT: C 342 PHE cc_start: 0.8434 (m-80) cc_final: 0.8039 (t80) REVERT: C 351 TYR cc_start: 0.7976 (p90) cc_final: 0.7292 (p90) REVERT: C 365 TYR cc_start: 0.7853 (m-80) cc_final: 0.7575 (m-80) REVERT: C 400 PHE cc_start: 0.7409 (p90) cc_final: 0.6918 (p90) REVERT: C 592 PHE cc_start: 0.7994 (p90) cc_final: 0.7771 (p90) REVERT: C 603 ASN cc_start: 0.6653 (t0) cc_final: 0.6345 (t0) REVERT: C 608 VAL cc_start: 0.8613 (t) cc_final: 0.8174 (p) REVERT: C 670 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8041 (pt) REVERT: C 722 VAL cc_start: 0.8847 (m) cc_final: 0.8617 (t) REVERT: C 772 VAL cc_start: 0.8402 (t) cc_final: 0.8196 (m) REVERT: C 784 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: C 825 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7997 (ttpp) REVERT: C 884 SER cc_start: 0.8641 (m) cc_final: 0.8422 (m) REVERT: C 949 GLN cc_start: 0.7647 (tp-100) cc_final: 0.7442 (tp-100) REVERT: C 1037 SER cc_start: 0.8195 (t) cc_final: 0.7896 (p) REVERT: D 332 MET cc_start: -0.0874 (ttm) cc_final: -0.1392 (ttm) REVERT: E 150 GLU cc_start: 0.3110 (tp30) cc_final: 0.2699 (tp30) REVERT: E 360 MET cc_start: 0.0030 (ttt) cc_final: -0.0438 (tpt) REVERT: E 366 MET cc_start: 0.3068 (tpt) cc_final: 0.1448 (tpt) REVERT: E 544 ILE cc_start: -0.0125 (OUTLIER) cc_final: -0.0507 (mm) outliers start: 129 outliers final: 88 residues processed: 628 average time/residue: 0.4118 time to fit residues: 428.5813 Evaluate side-chains 634 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 540 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 299 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 345 optimal weight: 20.0000 chunk 229 optimal weight: 0.9980 chunk 408 optimal weight: 20.0000 chunk 255 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 188 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 762 GLN B 913 GLN B 935 GLN C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4368 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 34220 Z= 0.311 Angle : 0.587 14.539 46636 Z= 0.293 Chirality : 0.047 0.489 5335 Planarity : 0.004 0.060 5997 Dihedral : 6.103 87.214 5368 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.53 % Allowed : 16.81 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.96 (0.13), residues: 4196 helix: 0.97 (0.15), residues: 1226 sheet: -0.49 (0.17), residues: 826 loop : -1.70 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 436 HIS 0.007 0.001 HIS A1064 PHE 0.027 0.002 PHE A 168 TYR 0.030 0.001 TYR A 170 ARG 0.006 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 543 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.8429 (m-80) cc_final: 0.8193 (m-80) REVERT: A 216 LEU cc_start: 0.7047 (mt) cc_final: 0.6791 (mt) REVERT: A 270 LEU cc_start: 0.8548 (mp) cc_final: 0.8342 (mp) REVERT: A 294 ASP cc_start: 0.6783 (p0) cc_final: 0.6522 (p0) REVERT: A 532 ASN cc_start: 0.5654 (OUTLIER) cc_final: 0.4622 (p0) REVERT: A 543 PHE cc_start: 0.7516 (m-10) cc_final: 0.7291 (m-10) REVERT: A 571 ASP cc_start: 0.6540 (t0) cc_final: 0.6177 (t0) REVERT: A 748 GLU cc_start: 0.6717 (mp0) cc_final: 0.6392 (mp0) REVERT: A 778 THR cc_start: 0.8874 (t) cc_final: 0.8652 (m) REVERT: A 872 GLN cc_start: 0.7745 (tt0) cc_final: 0.7530 (mt0) REVERT: A 957 GLN cc_start: 0.7410 (tt0) cc_final: 0.7113 (tt0) REVERT: A 1120 THR cc_start: 0.8440 (m) cc_final: 0.8225 (p) REVERT: A 1144 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6908 (mm-30) REVERT: B 48 LEU cc_start: 0.8359 (mt) cc_final: 0.8134 (mp) REVERT: B 50 SER cc_start: 0.8492 (m) cc_final: 0.8108 (p) REVERT: B 318 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8156 (p90) REVERT: B 549 THR cc_start: 0.8148 (m) cc_final: 0.7774 (p) REVERT: B 703 ASN cc_start: 0.7888 (t0) cc_final: 0.7550 (t0) REVERT: B 704 SER cc_start: 0.8297 (t) cc_final: 0.7924 (p) REVERT: B 708 SER cc_start: 0.7756 (t) cc_final: 0.7461 (m) REVERT: B 710 ASN cc_start: 0.8115 (p0) cc_final: 0.7765 (p0) REVERT: B 949 GLN cc_start: 0.7789 (tp40) cc_final: 0.7155 (tp40) REVERT: B 957 GLN cc_start: 0.7008 (tm-30) cc_final: 0.6786 (tm-30) REVERT: B 1029 MET cc_start: 0.8205 (tpp) cc_final: 0.7901 (ttm) REVERT: B 1118 ASP cc_start: 0.7361 (p0) cc_final: 0.7153 (p0) REVERT: C 51 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.7997 (p) REVERT: C 90 VAL cc_start: 0.8137 (t) cc_final: 0.7851 (p) REVERT: C 165 ASN cc_start: 0.3764 (OUTLIER) cc_final: 0.3376 (t0) REVERT: C 342 PHE cc_start: 0.8458 (m-80) cc_final: 0.7954 (t80) REVERT: C 351 TYR cc_start: 0.8029 (p90) cc_final: 0.7293 (p90) REVERT: C 365 TYR cc_start: 0.7847 (m-80) cc_final: 0.7537 (m-80) REVERT: C 400 PHE cc_start: 0.7401 (p90) cc_final: 0.6943 (p90) REVERT: C 440 LYS cc_start: 0.9074 (ttpp) cc_final: 0.8784 (ttpp) REVERT: C 538 CYS cc_start: 0.5482 (t) cc_final: 0.5133 (t) REVERT: C 592 PHE cc_start: 0.7996 (p90) cc_final: 0.7781 (p90) REVERT: C 603 ASN cc_start: 0.6650 (t0) cc_final: 0.6405 (t0) REVERT: C 608 VAL cc_start: 0.8645 (t) cc_final: 0.8205 (p) REVERT: C 670 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8075 (pt) REVERT: C 722 VAL cc_start: 0.8851 (m) cc_final: 0.8622 (t) REVERT: C 765 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7190 (ttp-110) REVERT: C 772 VAL cc_start: 0.8414 (t) cc_final: 0.8192 (m) REVERT: C 784 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7544 (mt0) REVERT: C 825 LYS cc_start: 0.8235 (ttpp) cc_final: 0.7995 (ttpp) REVERT: C 949 GLN cc_start: 0.7660 (tp-100) cc_final: 0.7444 (tp-100) REVERT: C 1005 GLN cc_start: 0.7720 (tp40) cc_final: 0.7511 (tp-100) REVERT: C 1037 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7903 (p) REVERT: D 332 MET cc_start: -0.0908 (ttm) cc_final: -0.1436 (ttm) REVERT: D 462 MET cc_start: 0.3020 (mmp) cc_final: 0.2280 (mmp) REVERT: E 298 MET cc_start: 0.4306 (tpt) cc_final: 0.4095 (tpt) REVERT: E 360 MET cc_start: 0.0138 (ttt) cc_final: -0.0433 (tpt) REVERT: E 366 MET cc_start: 0.3048 (tpt) cc_final: 0.1335 (tpt) REVERT: E 544 ILE cc_start: -0.0137 (OUTLIER) cc_final: -0.0510 (mm) outliers start: 123 outliers final: 99 residues processed: 616 average time/residue: 0.4200 time to fit residues: 431.8751 Evaluate side-chains 628 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 521 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 79 optimal weight: 0.2980 chunk 259 optimal weight: 0.0010 chunk 278 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 38 optimal weight: 30.0000 chunk 321 optimal weight: 4.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1135 ASN B 115 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 762 GLN B 913 GLN B 935 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4342 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34220 Z= 0.201 Angle : 0.557 14.005 46636 Z= 0.277 Chirality : 0.045 0.442 5335 Planarity : 0.004 0.048 5997 Dihedral : 5.832 84.839 5368 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.33 % Allowed : 17.41 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4196 helix: 1.11 (0.15), residues: 1236 sheet: -0.36 (0.18), residues: 809 loop : -1.59 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 436 HIS 0.012 0.001 HIS E 353 PHE 0.025 0.001 PHE B 970 TYR 0.027 0.001 TYR A 170 ARG 0.009 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 534 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7207 (p) cc_final: 0.6299 (t) REVERT: A 204 TYR cc_start: 0.8413 (m-80) cc_final: 0.8177 (m-80) REVERT: A 216 LEU cc_start: 0.7031 (mt) cc_final: 0.6785 (mt) REVERT: A 294 ASP cc_start: 0.6788 (p0) cc_final: 0.6542 (p0) REVERT: A 571 ASP cc_start: 0.6508 (t0) cc_final: 0.6180 (t0) REVERT: A 748 GLU cc_start: 0.6684 (mp0) cc_final: 0.6354 (mp0) REVERT: A 778 THR cc_start: 0.8927 (t) cc_final: 0.8698 (m) REVERT: A 872 GLN cc_start: 0.7717 (tt0) cc_final: 0.7493 (mt0) REVERT: A 995 ARG cc_start: 0.7331 (ttm-80) cc_final: 0.7061 (ttm170) REVERT: A 1019 ARG cc_start: 0.7257 (ttp80) cc_final: 0.7021 (ttp-170) REVERT: A 1055 SER cc_start: 0.8171 (m) cc_final: 0.7965 (t) REVERT: A 1144 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6906 (mm-30) REVERT: B 48 LEU cc_start: 0.8344 (mt) cc_final: 0.8115 (mp) REVERT: B 50 SER cc_start: 0.8469 (m) cc_final: 0.8079 (p) REVERT: B 318 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8091 (p90) REVERT: B 549 THR cc_start: 0.8061 (m) cc_final: 0.7669 (p) REVERT: B 704 SER cc_start: 0.8244 (t) cc_final: 0.7914 (p) REVERT: B 710 ASN cc_start: 0.8087 (p0) cc_final: 0.7723 (p0) REVERT: B 949 GLN cc_start: 0.7819 (tp40) cc_final: 0.7586 (tp40) REVERT: B 1029 MET cc_start: 0.8179 (tpp) cc_final: 0.7892 (ttm) REVERT: B 1118 ASP cc_start: 0.7346 (p0) cc_final: 0.7115 (p0) REVERT: C 51 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7967 (p) REVERT: C 90 VAL cc_start: 0.8081 (t) cc_final: 0.7786 (p) REVERT: C 165 ASN cc_start: 0.3732 (OUTLIER) cc_final: 0.3355 (t0) REVERT: C 342 PHE cc_start: 0.8444 (m-80) cc_final: 0.7997 (t80) REVERT: C 365 TYR cc_start: 0.7812 (m-80) cc_final: 0.7455 (m-80) REVERT: C 400 PHE cc_start: 0.7397 (p90) cc_final: 0.6945 (p90) REVERT: C 418 ILE cc_start: 0.8058 (mt) cc_final: 0.7798 (mp) REVERT: C 440 LYS cc_start: 0.9088 (ttpp) cc_final: 0.8769 (ttpp) REVERT: C 592 PHE cc_start: 0.7991 (p90) cc_final: 0.7763 (p90) REVERT: C 603 ASN cc_start: 0.6620 (t0) cc_final: 0.6348 (t0) REVERT: C 608 VAL cc_start: 0.8614 (t) cc_final: 0.8190 (p) REVERT: C 670 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8080 (pt) REVERT: C 772 VAL cc_start: 0.8421 (t) cc_final: 0.8174 (m) REVERT: C 825 LYS cc_start: 0.8213 (ttpp) cc_final: 0.7967 (ttpp) REVERT: C 949 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7408 (tp-100) REVERT: C 1037 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7922 (p) REVERT: D 332 MET cc_start: -0.0985 (ttm) cc_final: -0.1457 (ttm) REVERT: D 462 MET cc_start: 0.2901 (mmp) cc_final: 0.2240 (mmp) REVERT: E 150 GLU cc_start: 0.2905 (tp30) cc_final: 0.2469 (tp30) REVERT: E 270 MET cc_start: 0.3698 (mtm) cc_final: 0.3271 (mtm) REVERT: E 360 MET cc_start: 0.0121 (ttt) cc_final: -0.0457 (tpt) REVERT: E 366 MET cc_start: 0.3012 (tpt) cc_final: 0.1256 (tpt) REVERT: E 544 ILE cc_start: -0.0128 (OUTLIER) cc_final: -0.0502 (mm) outliers start: 116 outliers final: 85 residues processed: 611 average time/residue: 0.4117 time to fit residues: 418.7315 Evaluate side-chains 610 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 519 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 10.0000 chunk 391 optimal weight: 0.0070 chunk 357 optimal weight: 50.0000 chunk 380 optimal weight: 6.9990 chunk 229 optimal weight: 0.7980 chunk 165 optimal weight: 0.5980 chunk 299 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 344 optimal weight: 30.0000 chunk 360 optimal weight: 10.0000 chunk 379 optimal weight: 10.0000 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 762 GLN B 913 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4360 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34220 Z= 0.258 Angle : 0.571 14.941 46636 Z= 0.284 Chirality : 0.046 0.559 5335 Planarity : 0.004 0.049 5997 Dihedral : 5.759 82.604 5368 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.02 % Allowed : 17.96 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.73 (0.13), residues: 4196 helix: 1.19 (0.15), residues: 1222 sheet: -0.44 (0.17), residues: 813 loop : -1.53 (0.12), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 436 HIS 0.011 0.001 HIS C 49 PHE 0.027 0.002 PHE C 168 TYR 0.027 0.001 TYR A 170 ARG 0.009 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 522 time to evaluate : 3.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7273 (p) cc_final: 0.6289 (t) REVERT: A 204 TYR cc_start: 0.8405 (m-80) cc_final: 0.8174 (m-80) REVERT: A 216 LEU cc_start: 0.7058 (mt) cc_final: 0.6803 (mt) REVERT: A 294 ASP cc_start: 0.6803 (p0) cc_final: 0.6536 (p0) REVERT: A 532 ASN cc_start: 0.5582 (OUTLIER) cc_final: 0.4532 (p0) REVERT: A 571 ASP cc_start: 0.6550 (t0) cc_final: 0.6233 (t0) REVERT: A 748 GLU cc_start: 0.6702 (mp0) cc_final: 0.6388 (mp0) REVERT: A 778 THR cc_start: 0.8903 (t) cc_final: 0.8685 (m) REVERT: A 872 GLN cc_start: 0.7784 (tt0) cc_final: 0.7550 (mt0) REVERT: A 1055 SER cc_start: 0.8166 (m) cc_final: 0.7961 (t) REVERT: A 1144 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6871 (mm-30) REVERT: B 48 LEU cc_start: 0.8373 (mt) cc_final: 0.8144 (mp) REVERT: B 50 SER cc_start: 0.8469 (m) cc_final: 0.8103 (p) REVERT: B 318 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8075 (p90) REVERT: B 549 THR cc_start: 0.8099 (m) cc_final: 0.7723 (p) REVERT: B 703 ASN cc_start: 0.7887 (t0) cc_final: 0.7597 (t0) REVERT: B 704 SER cc_start: 0.8285 (t) cc_final: 0.7914 (p) REVERT: B 710 ASN cc_start: 0.8069 (p0) cc_final: 0.7753 (p0) REVERT: B 949 GLN cc_start: 0.7876 (tp40) cc_final: 0.7299 (tp40) REVERT: B 1029 MET cc_start: 0.8187 (tpp) cc_final: 0.7920 (ttm) REVERT: B 1118 ASP cc_start: 0.7348 (p0) cc_final: 0.7121 (p0) REVERT: C 51 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7943 (p) REVERT: C 90 VAL cc_start: 0.8113 (t) cc_final: 0.7822 (p) REVERT: C 165 ASN cc_start: 0.3746 (OUTLIER) cc_final: 0.3331 (t0) REVERT: C 342 PHE cc_start: 0.8465 (m-80) cc_final: 0.8023 (t80) REVERT: C 355 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7399 (mtt180) REVERT: C 365 TYR cc_start: 0.7836 (m-80) cc_final: 0.7516 (m-80) REVERT: C 400 PHE cc_start: 0.7408 (p90) cc_final: 0.6943 (p90) REVERT: C 418 ILE cc_start: 0.8087 (mt) cc_final: 0.7812 (mp) REVERT: C 440 LYS cc_start: 0.9050 (ttpp) cc_final: 0.8793 (ttpp) REVERT: C 538 CYS cc_start: 0.5434 (t) cc_final: 0.5104 (t) REVERT: C 578 ASP cc_start: 0.6874 (p0) cc_final: 0.6651 (p0) REVERT: C 592 PHE cc_start: 0.7994 (p90) cc_final: 0.7777 (p90) REVERT: C 603 ASN cc_start: 0.6640 (t0) cc_final: 0.6379 (t0) REVERT: C 608 VAL cc_start: 0.8652 (t) cc_final: 0.8222 (p) REVERT: C 670 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8116 (pt) REVERT: C 772 VAL cc_start: 0.8435 (t) cc_final: 0.8211 (m) REVERT: C 825 LYS cc_start: 0.8234 (ttpp) cc_final: 0.7989 (ttpp) REVERT: C 949 GLN cc_start: 0.7687 (tp-100) cc_final: 0.7472 (tp-100) REVERT: C 1037 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7923 (p) REVERT: D 332 MET cc_start: -0.0940 (ttm) cc_final: -0.1499 (ttm) REVERT: D 462 MET cc_start: 0.2855 (mmp) cc_final: 0.2191 (mmp) REVERT: E 270 MET cc_start: 0.3698 (mtm) cc_final: 0.3278 (mtm) REVERT: E 360 MET cc_start: 0.0030 (ttt) cc_final: -0.0343 (tpt) REVERT: E 366 MET cc_start: 0.2890 (tpt) cc_final: 0.1128 (tpt) REVERT: E 544 ILE cc_start: -0.0082 (OUTLIER) cc_final: -0.0472 (mm) outliers start: 105 outliers final: 89 residues processed: 594 average time/residue: 0.4132 time to fit residues: 408.6662 Evaluate side-chains 612 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 516 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 0.7980 chunk 402 optimal weight: 0.9990 chunk 245 optimal weight: 0.0970 chunk 191 optimal weight: 0.8980 chunk 279 optimal weight: 0.7980 chunk 422 optimal weight: 50.0000 chunk 388 optimal weight: 30.0000 chunk 336 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 259 optimal weight: 0.1980 chunk 206 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 755 GLN B 762 GLN B 913 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 196 ASN C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4347 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34220 Z= 0.205 Angle : 0.557 14.247 46636 Z= 0.277 Chirality : 0.046 0.639 5335 Planarity : 0.004 0.049 5997 Dihedral : 5.625 79.910 5368 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.84 % Allowed : 18.22 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4196 helix: 1.21 (0.15), residues: 1236 sheet: -0.33 (0.18), residues: 799 loop : -1.47 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 436 HIS 0.010 0.001 HIS C 49 PHE 0.031 0.001 PHE A 643 TYR 0.027 0.001 TYR A 170 ARG 0.009 0.000 ARG B 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 525 time to evaluate : 3.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8175 (mt) cc_final: 0.7922 (mm) REVERT: A 63 THR cc_start: 0.7181 (p) cc_final: 0.6314 (t) REVERT: A 204 TYR cc_start: 0.8395 (m-80) cc_final: 0.8157 (m-80) REVERT: A 216 LEU cc_start: 0.7062 (mt) cc_final: 0.6830 (mt) REVERT: A 532 ASN cc_start: 0.5531 (OUTLIER) cc_final: 0.4500 (p0) REVERT: A 571 ASP cc_start: 0.6582 (t0) cc_final: 0.6262 (t0) REVERT: A 748 GLU cc_start: 0.6665 (mp0) cc_final: 0.6368 (mp0) REVERT: A 778 THR cc_start: 0.8892 (t) cc_final: 0.8668 (m) REVERT: A 872 GLN cc_start: 0.7732 (tt0) cc_final: 0.7506 (mt0) REVERT: A 1144 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6808 (mm-30) REVERT: B 48 LEU cc_start: 0.8366 (mt) cc_final: 0.8147 (mp) REVERT: B 50 SER cc_start: 0.8464 (m) cc_final: 0.8096 (p) REVERT: B 318 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8092 (p90) REVERT: B 549 THR cc_start: 0.8095 (m) cc_final: 0.7714 (p) REVERT: B 703 ASN cc_start: 0.7880 (t0) cc_final: 0.7609 (t0) REVERT: B 710 ASN cc_start: 0.8064 (p0) cc_final: 0.7728 (p0) REVERT: B 949 GLN cc_start: 0.7908 (tp40) cc_final: 0.7506 (tp40) REVERT: B 1029 MET cc_start: 0.8184 (tpp) cc_final: 0.7894 (ttm) REVERT: B 1118 ASP cc_start: 0.7330 (p0) cc_final: 0.7115 (p0) REVERT: C 51 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7941 (p) REVERT: C 90 VAL cc_start: 0.8078 (t) cc_final: 0.7798 (p) REVERT: C 165 ASN cc_start: 0.3649 (OUTLIER) cc_final: 0.3392 (t0) REVERT: C 342 PHE cc_start: 0.8461 (m-80) cc_final: 0.8021 (t80) REVERT: C 355 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7398 (mtt180) REVERT: C 365 TYR cc_start: 0.7830 (m-80) cc_final: 0.7599 (m-80) REVERT: C 400 PHE cc_start: 0.7401 (p90) cc_final: 0.6964 (p90) REVERT: C 418 ILE cc_start: 0.8103 (mt) cc_final: 0.7836 (mp) REVERT: C 440 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8795 (ttpp) REVERT: C 538 CYS cc_start: 0.5453 (t) cc_final: 0.5127 (t) REVERT: C 578 ASP cc_start: 0.6921 (p0) cc_final: 0.6714 (p0) REVERT: C 592 PHE cc_start: 0.7987 (p90) cc_final: 0.7766 (p90) REVERT: C 603 ASN cc_start: 0.6637 (t0) cc_final: 0.6366 (t0) REVERT: C 608 VAL cc_start: 0.8645 (t) cc_final: 0.8208 (p) REVERT: C 670 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8149 (pt) REVERT: C 772 VAL cc_start: 0.8462 (t) cc_final: 0.8198 (m) REVERT: C 825 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7965 (ttpp) REVERT: C 949 GLN cc_start: 0.7652 (tp-100) cc_final: 0.7439 (tp-100) REVERT: C 1037 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7949 (p) REVERT: D 332 MET cc_start: -0.1046 (ttm) cc_final: -0.1602 (ttm) REVERT: D 462 MET cc_start: 0.2761 (mmp) cc_final: 0.2078 (mmp) REVERT: E 270 MET cc_start: 0.3683 (mtm) cc_final: 0.3283 (mtm) REVERT: E 298 MET cc_start: 0.4043 (mmm) cc_final: 0.3468 (tpt) REVERT: E 360 MET cc_start: 0.0060 (ttt) cc_final: -0.0320 (tpt) REVERT: E 366 MET cc_start: 0.2871 (tpt) cc_final: 0.1105 (tpt) REVERT: E 544 ILE cc_start: -0.0070 (OUTLIER) cc_final: -0.0465 (mm) outliers start: 99 outliers final: 87 residues processed: 591 average time/residue: 0.4218 time to fit residues: 415.4215 Evaluate side-chains 605 residues out of total 3713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 511 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 267 optimal weight: 0.9980 chunk 358 optimal weight: 40.0000 chunk 103 optimal weight: 0.1980 chunk 310 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 336 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 345 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 755 GLN B 913 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.238405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.172707 restraints weight = 53099.585| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.09 r_work: 0.3534 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 34220 Z= 0.273 Angle : 0.760 59.161 46636 Z= 0.423 Chirality : 0.051 1.186 5335 Planarity : 0.004 0.088 5997 Dihedral : 5.617 79.894 5368 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.82 % Allowed : 18.33 % Favored : 78.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4196 helix: 1.21 (0.15), residues: 1236 sheet: -0.33 (0.18), residues: 799 loop : -1.47 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 436 HIS 0.008 0.001 HIS C 49 PHE 0.025 0.001 PHE A 643 TYR 0.025 0.001 TYR A 170 ARG 0.004 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9061.87 seconds wall clock time: 163 minutes 2.44 seconds (9782.44 seconds total)