Starting phenix.real_space_refine on Tue Feb 20 07:21:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/02_2024/7k8y_22735.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/02_2024/7k8y_22735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/02_2024/7k8y_22735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/02_2024/7k8y_22735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/02_2024/7k8y_22735.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/02_2024/7k8y_22735.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1619 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 16284 2.51 5 N 4219 2.21 5 O 4941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 198": "OD1" <-> "OD2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 346": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ASP 442": "OD1" <-> "OD2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 457": "NH1" <-> "NH2" Residue "D PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 571": "OD1" <-> "OD2" Residue "D TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 936": "OD1" <-> "OD2" Residue "D ASP 1041": "OD1" <-> "OD2" Residue "D TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E ARG 457": "NH1" <-> "NH2" Residue "E PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 773": "OE1" <-> "OE2" Residue "E PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 988": "OE1" <-> "OE2" Residue "E ASP 994": "OD1" <-> "OD2" Residue "E GLU 1017": "OE1" <-> "OE2" Residue "E TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1092": "OE1" <-> "OE2" Residue "E PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25560 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "D" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "E" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'CIS': 2, 'PTRANS': 49, 'TRANS': 950} Chain breaks: 7 Chain: "G" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 121} Chain: "I" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 778 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.16, per 1000 atoms: 0.51 Number of scatterers: 25560 At special positions: 0 Unit cell: (141.284, 144.628, 204.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 4941 8.00 N 4219 7.00 C 16284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.04 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.04 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " 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=1, symmetry=0 Links applied NAG-ASN " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG D1301 " - " ASN D 282 " " NAG D1302 " - " ASN D 331 " " NAG D1303 " - " ASN D 603 " " NAG D1304 " - " ASN D 616 " " NAG D1305 " - " ASN D 709 " " NAG D1306 " - " ASN D 717 " " NAG D1307 " - " ASN D 801 " " NAG D1308 " - " ASN D1134 " " NAG E1301 " - " ASN E 122 " " NAG E1302 " - " ASN E 282 " " NAG E1303 " - " ASN E 331 " " NAG E1304 " - " ASN E 616 " " NAG E1305 " - " ASN E 709 " " NAG E1306 " - " ASN E 717 " " NAG E1307 " - " ASN E 801 " " NAG E1308 " - " ASN E1074 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.30 Conformation dependent library (CDL) restraints added in 5.1 seconds 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6048 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 50 sheets defined 24.3% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.962A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.522A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.522A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.627A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.353A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.314A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.996A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.618A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.859A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 388' Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.848A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE D 410 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.822A pdb=" N GLN D 506 " --> pdb=" O VAL D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 744 removed outlier: 3.563A pdb=" N GLY D 744 " --> pdb=" O MET D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.988A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.733A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 Processing helix chain 'D' and resid 912 through 941 removed outlier: 4.351A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 966 removed outlier: 4.344A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 984 removed outlier: 4.134A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.856A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1118 No H-bonds generated for 'chain 'D' and resid 1116 through 1118' Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 3.976A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.312A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 747 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 891 removed outlier: 3.830A pdb=" N ALA E 890 " --> pdb=" O TRP E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 966 removed outlier: 4.152A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.726A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.529A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1147 removed outlier: 3.874A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.598A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.758A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.623A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.925A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.306A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.731A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.334A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.690A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.961A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.689A pdb=" N ALA B 701 " --> pdb=" O ILE D 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.472A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.472A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.368A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 28 through 29 removed outlier: 6.519A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.994A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'D' and resid 141 through 142 removed outlier: 6.392A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 311 through 313 Processing sheet with id=AC4, first strand: chain 'D' and resid 325 through 328 removed outlier: 5.356A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE D 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.644A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 701 through 702 removed outlier: 7.081A pdb=" N ALA D 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'D' and resid 718 through 728 removed outlier: 6.839A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 734 through 735 Processing sheet with id=AD4, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.377A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS D1088 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 28 through 31 removed outlier: 3.723A pdb=" N SER E 60 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 47 through 55 removed outlier: 4.049A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.021A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 84 through 85 removed outlier: 5.784A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.475A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AE3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.079A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 712 through 728 removed outlier: 6.837A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.315A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AF4, first strand: chain 'I' and resid 9 through 13 removed outlier: 6.490A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 19 through 24 1096 hydrogen bonds defined for protein. 2979 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.91 Time building geometry restraints manager: 10.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8199 1.35 - 1.47: 6559 1.47 - 1.59: 11225 1.59 - 1.72: 1 1.72 - 1.84: 146 Bond restraints: 26130 Sorted by residual: bond pdb=" CA PHE I 98 " pdb=" C PHE I 98 " ideal model delta sigma weight residual 1.525 1.595 -0.070 1.25e-02 6.40e+03 3.14e+01 bond pdb=" CA VAL I 97 " pdb=" C VAL I 97 " ideal model delta sigma weight residual 1.523 1.592 -0.069 1.27e-02 6.20e+03 2.93e+01 bond pdb=" N PHE I 98 " pdb=" CA PHE I 98 " ideal model delta sigma weight residual 1.458 1.521 -0.063 1.42e-02 4.96e+03 1.96e+01 bond pdb=" N VAL I 97 " pdb=" CA VAL I 97 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.41e+01 bond pdb=" C1 NAG E1307 " pdb=" O5 NAG E1307 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 26125 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.87: 748 106.87 - 113.68: 14252 113.68 - 120.49: 9734 120.49 - 127.30: 10594 127.30 - 134.11: 223 Bond angle restraints: 35551 Sorted by residual: angle pdb=" N PHE I 98 " pdb=" CA PHE I 98 " pdb=" C PHE I 98 " ideal model delta sigma weight residual 108.24 125.89 -17.65 1.32e+00 5.74e-01 1.79e+02 angle pdb=" C PHE I 98 " pdb=" N GLY I 99 " pdb=" CA GLY I 99 " ideal model delta sigma weight residual 121.96 130.85 -8.89 1.38e+00 5.25e-01 4.15e+01 angle pdb=" N THR G 104 " pdb=" CA THR G 104 " pdb=" C THR G 104 " ideal model delta sigma weight residual 113.17 106.20 6.97 1.26e+00 6.30e-01 3.06e+01 angle pdb=" N TYR G 115 " pdb=" CA TYR G 115 " pdb=" C TYR G 115 " ideal model delta sigma weight residual 108.38 114.73 -6.35 1.35e+00 5.49e-01 2.22e+01 angle pdb=" N THR E 124 " pdb=" CA THR E 124 " pdb=" C THR E 124 " ideal model delta sigma weight residual 114.75 109.06 5.69 1.26e+00 6.30e-01 2.04e+01 ... (remaining 35546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.70: 15334 24.70 - 49.40: 437 49.40 - 74.10: 52 74.10 - 98.80: 20 98.80 - 123.49: 1 Dihedral angle restraints: 15844 sinusoidal: 6434 harmonic: 9410 Sorted by residual: dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 760 " pdb=" CB CYS E 760 " ideal model delta sinusoidal sigma weight residual 93.00 4.25 88.75 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 5.04 87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -173.52 87.52 1 1.00e+01 1.00e-02 9.18e+01 ... (remaining 15841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4077 0.123 - 0.246: 23 0.246 - 0.369: 7 0.369 - 0.491: 2 0.491 - 0.614: 2 Chirality restraints: 4111 Sorted by residual: chirality pdb=" C1 NAG E1305 " pdb=" ND2 ASN E 709 " pdb=" C2 NAG E1305 " pdb=" O5 NAG E1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.43e+00 chirality pdb=" C1 NAG D1302 " pdb=" ND2 ASN D 331 " pdb=" C2 NAG D1302 " pdb=" O5 NAG D1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" C1 NAG E1306 " pdb=" ND2 ASN E 717 " pdb=" C2 NAG E1306 " pdb=" O5 NAG E1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.86 0.46 2.00e-01 2.50e+01 5.36e+00 ... (remaining 4108 not shown) Planarity restraints: 4594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 717 " -0.034 2.00e-02 2.50e+03 8.07e-02 8.14e+01 pdb=" CG ASN E 717 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN E 717 " 0.081 2.00e-02 2.50e+03 pdb=" ND2 ASN E 717 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG E1306 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 122 " 0.046 2.00e-02 2.50e+03 5.41e-02 3.66e+01 pdb=" CG ASN E 122 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN E 122 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN E 122 " -0.086 2.00e-02 2.50e+03 pdb=" C1 NAG E1301 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 282 " -0.045 2.00e-02 2.50e+03 5.15e-02 3.31e+01 pdb=" CG ASN D 282 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN D 282 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 282 " 0.086 2.00e-02 2.50e+03 pdb=" C1 NAG D1301 " -0.060 2.00e-02 2.50e+03 ... (remaining 4591 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 22 1.89 - 2.64: 521 2.64 - 3.39: 33951 3.39 - 4.15: 61462 4.15 - 4.90: 108946 Nonbonded interactions: 204902 Sorted by model distance: nonbonded pdb=" O ALA D 713 " pdb=" CG LEU E 894 " model vdw 1.137 3.470 nonbonded pdb=" O ALA D 713 " pdb=" CD1 LEU E 894 " model vdw 1.340 3.460 nonbonded pdb=" OE2 GLU B 516 " pdb=" OH TYR D 200 " model vdw 1.368 2.440 nonbonded pdb=" CE1 PHE D 559 " pdb=" CD2 PHE E 43 " model vdw 1.370 3.640 nonbonded pdb=" CH2 TRP G 47 " pdb=" OG SER I 95 " model vdw 1.387 3.340 ... (remaining 204897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 27 through 1147 or resid 1301 through 1307)) selection = (chain 'E' and (resid 27 through 1147 or resid 1301 through 1307)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 19.950 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 73.000 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 26130 Z= 0.178 Angle : 0.546 17.652 35551 Z= 0.313 Chirality : 0.046 0.614 4111 Planarity : 0.004 0.048 4571 Dihedral : 10.962 123.494 9679 Min Nonbonded Distance : 1.137 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.79 % Favored : 96.96 % Rotamer: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.13), residues: 3190 helix: -0.03 (0.19), residues: 641 sheet: -0.91 (0.17), residues: 767 loop : -2.22 (0.12), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 120 HIS 0.003 0.000 HIS E1048 PHE 0.008 0.001 PHE B 192 TYR 0.023 0.001 TYR G 115 ARG 0.006 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 3.258 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: B 406 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9223 (mp0) REVERT: B 902 MET cc_start: 0.9817 (mmm) cc_final: 0.9419 (mmp) REVERT: B 964 LYS cc_start: 0.9843 (tppt) cc_final: 0.9639 (mmmt) REVERT: B 966 LEU cc_start: 0.9554 (mt) cc_final: 0.9352 (mp) REVERT: B 1018 ILE cc_start: 0.9715 (mm) cc_final: 0.9484 (tp) REVERT: B 1062 PHE cc_start: 0.9722 (m-80) cc_final: 0.9319 (m-80) REVERT: D 552 LEU cc_start: 0.9277 (mt) cc_final: 0.9027 (mm) REVERT: D 902 MET cc_start: 0.9751 (mmm) cc_final: 0.9549 (mmp) REVERT: D 936 ASP cc_start: 0.9111 (m-30) cc_final: 0.8833 (t0) REVERT: D 960 ASN cc_start: 0.9189 (m-40) cc_final: 0.8750 (m110) REVERT: D 1029 MET cc_start: 0.9615 (tpp) cc_final: 0.9374 (tpp) REVERT: E 203 ILE cc_start: 0.9702 (mt) cc_final: 0.9257 (mt) REVERT: E 227 VAL cc_start: 0.8783 (t) cc_final: 0.8535 (t) REVERT: E 270 LEU cc_start: 0.9024 (mt) cc_final: 0.8799 (mt) REVERT: E 495 TYR cc_start: 0.4988 (m-10) cc_final: 0.4337 (m-80) REVERT: E 606 ASN cc_start: 0.8857 (p0) cc_final: 0.8638 (p0) REVERT: E 773 GLU cc_start: 0.9214 (pt0) cc_final: 0.8970 (pp20) REVERT: E 782 PHE cc_start: 0.9182 (m-80) cc_final: 0.8570 (m-80) REVERT: E 802 PHE cc_start: 0.9253 (m-80) cc_final: 0.8862 (m-80) REVERT: E 805 ILE cc_start: 0.9783 (pt) cc_final: 0.9449 (tp) REVERT: E 869 MET cc_start: 0.9130 (mtt) cc_final: 0.8722 (mtt) REVERT: E 902 MET cc_start: 0.9656 (mmm) cc_final: 0.9414 (mmm) REVERT: E 934 ILE cc_start: 0.9351 (mm) cc_final: 0.9086 (pt) REVERT: E 964 LYS cc_start: 0.9654 (mmmt) cc_final: 0.9431 (mmmt) REVERT: E 1029 MET cc_start: 0.9345 (tpp) cc_final: 0.8981 (tpp) REVERT: E 1034 LEU cc_start: 0.9599 (mp) cc_final: 0.9390 (mp) outliers start: 1 outliers final: 1 residues processed: 274 average time/residue: 0.4240 time to fit residues: 177.6378 Evaluate side-chains 154 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 252 optimal weight: 0.0980 chunk 97 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 292 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 314 GLN B 394 ASN B 437 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 777 ASN B 953 ASN B 965 GLN B1002 GLN D 66 HIS ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN D 762 GLN ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN D 935 GLN E 450 ASN E 542 ASN E 675 GLN ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 965 GLN G 39 GLN I 6 GLN I 79 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26130 Z= 0.188 Angle : 0.530 12.043 35551 Z= 0.272 Chirality : 0.042 0.215 4111 Planarity : 0.004 0.053 4571 Dihedral : 6.198 106.459 3949 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.23 % Favored : 96.58 % Rotamer: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3190 helix: 1.55 (0.21), residues: 641 sheet: -0.59 (0.17), residues: 770 loop : -1.61 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 50 HIS 0.006 0.001 HIS E1048 PHE 0.027 0.001 PHE E 559 TYR 0.023 0.001 TYR G 115 ARG 0.006 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 2.818 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: B 406 GLU cc_start: 0.9452 (mm-30) cc_final: 0.9068 (mp0) REVERT: B 697 MET cc_start: 0.7882 (ptp) cc_final: 0.6906 (ptp) REVERT: B 867 ASP cc_start: 0.9396 (p0) cc_final: 0.8709 (t0) REVERT: B 869 MET cc_start: 0.9480 (mtm) cc_final: 0.9236 (mtt) REVERT: B 902 MET cc_start: 0.9860 (mmm) cc_final: 0.9400 (mmp) REVERT: B 1018 ILE cc_start: 0.9832 (mm) cc_final: 0.9545 (tp) REVERT: B 1062 PHE cc_start: 0.9696 (m-80) cc_final: 0.9400 (m-10) REVERT: D 387 LEU cc_start: 0.8486 (pp) cc_final: 0.7914 (mt) REVERT: D 552 LEU cc_start: 0.9364 (mt) cc_final: 0.9129 (mm) REVERT: D 731 MET cc_start: 0.9107 (ppp) cc_final: 0.8876 (ppp) REVERT: D 936 ASP cc_start: 0.9192 (m-30) cc_final: 0.8911 (t0) REVERT: E 227 VAL cc_start: 0.8833 (t) cc_final: 0.8587 (t) REVERT: E 270 LEU cc_start: 0.9208 (mt) cc_final: 0.9004 (mt) REVERT: E 495 TYR cc_start: 0.5139 (m-10) cc_final: 0.4824 (m-80) REVERT: E 606 ASN cc_start: 0.8989 (p0) cc_final: 0.8744 (p0) REVERT: E 770 ILE cc_start: 0.9760 (mt) cc_final: 0.9430 (mt) REVERT: E 773 GLU cc_start: 0.9346 (pt0) cc_final: 0.9015 (pp20) REVERT: E 782 PHE cc_start: 0.9376 (m-80) cc_final: 0.8723 (m-80) REVERT: E 869 MET cc_start: 0.9444 (mtt) cc_final: 0.9107 (mtt) REVERT: E 902 MET cc_start: 0.9657 (mmm) cc_final: 0.9382 (mmp) REVERT: E 964 LYS cc_start: 0.9724 (mmmt) cc_final: 0.9514 (mmmt) REVERT: E 966 LEU cc_start: 0.9404 (mt) cc_final: 0.9013 (mp) REVERT: E 1001 LEU cc_start: 0.9849 (tp) cc_final: 0.9482 (tp) REVERT: E 1041 ASP cc_start: 0.8836 (t0) cc_final: 0.8361 (t0) REVERT: I 62 PHE cc_start: 0.7729 (m-10) cc_final: 0.7403 (m-10) REVERT: I 69 ASN cc_start: 0.9411 (m-40) cc_final: 0.9205 (t0) outliers start: 3 outliers final: 0 residues processed: 182 average time/residue: 0.3925 time to fit residues: 112.0157 Evaluate side-chains 127 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 290 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 235 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN D 314 GLN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN D 655 HIS D 751 ASN ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 ASN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN E 655 HIS E 784 GLN E 804 GLN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 935 GLN ** E 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 953 ASN E 955 ASN E1119 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 26130 Z= 0.426 Angle : 0.776 13.316 35551 Z= 0.407 Chirality : 0.046 0.252 4111 Planarity : 0.005 0.085 4571 Dihedral : 6.946 88.538 3949 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.02 % Favored : 94.80 % Rotamer: Outliers : 0.18 % Allowed : 6.07 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3190 helix: 0.71 (0.20), residues: 670 sheet: -0.78 (0.17), residues: 768 loop : -1.51 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 886 HIS 0.015 0.002 HIS I 39 PHE 0.030 0.003 PHE B1052 TYR 0.022 0.002 TYR G 115 ARG 0.007 0.001 ARG E 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9056 (mp0) REVERT: B 869 MET cc_start: 0.9649 (mtm) cc_final: 0.9131 (mtp) REVERT: B 902 MET cc_start: 0.9892 (mmm) cc_final: 0.9506 (mmp) REVERT: B 1034 LEU cc_start: 0.9848 (mp) cc_final: 0.9611 (mp) REVERT: B 1062 PHE cc_start: 0.9754 (m-80) cc_final: 0.9390 (m-10) REVERT: D 277 LEU cc_start: 0.9746 (mp) cc_final: 0.9314 (tt) REVERT: D 731 MET cc_start: 0.9169 (ppp) cc_final: 0.8736 (ppp) REVERT: D 1029 MET cc_start: 0.9823 (tpt) cc_final: 0.9577 (tpp) REVERT: E 104 TRP cc_start: 0.9280 (m100) cc_final: 0.8632 (m100) REVERT: E 568 ASP cc_start: 0.9728 (t0) cc_final: 0.9195 (m-30) REVERT: E 869 MET cc_start: 0.9531 (mtt) cc_final: 0.9205 (mtt) REVERT: E 902 MET cc_start: 0.9721 (mmm) cc_final: 0.9440 (mmp) REVERT: E 964 LYS cc_start: 0.9836 (mmmt) cc_final: 0.9591 (mmmt) REVERT: E 1001 LEU cc_start: 0.9848 (tp) cc_final: 0.9616 (tt) REVERT: E 1062 PHE cc_start: 0.9668 (m-80) cc_final: 0.9359 (m-10) REVERT: I 46 LEU cc_start: 0.8222 (tp) cc_final: 0.8016 (tp) REVERT: I 47 MET cc_start: 0.8440 (mmp) cc_final: 0.8004 (mmm) REVERT: I 54 ARG cc_start: 0.3781 (mtt90) cc_final: 0.3581 (mtm-85) REVERT: I 62 PHE cc_start: 0.7769 (m-10) cc_final: 0.7420 (m-10) REVERT: I 69 ASN cc_start: 0.9456 (m-40) cc_final: 0.9250 (t0) outliers start: 5 outliers final: 2 residues processed: 125 average time/residue: 0.3708 time to fit residues: 76.1027 Evaluate side-chains 91 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 139 optimal weight: 0.0370 chunk 196 optimal weight: 4.9990 chunk 293 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 474 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B 965 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1048 HIS ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 953 ASN E 955 ASN I 6 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26130 Z= 0.193 Angle : 0.558 11.666 35551 Z= 0.285 Chirality : 0.043 0.228 4111 Planarity : 0.004 0.037 4571 Dihedral : 6.098 62.071 3949 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.01 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3190 helix: 1.55 (0.21), residues: 676 sheet: -0.51 (0.17), residues: 759 loop : -1.41 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 50 HIS 0.005 0.001 HIS E1048 PHE 0.018 0.001 PHE E 306 TYR 0.016 0.001 TYR G 112 ARG 0.004 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.100 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: B 406 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9079 (mp0) REVERT: B 731 MET cc_start: 0.9575 (ptp) cc_final: 0.9341 (ptp) REVERT: B 740 MET cc_start: 0.9354 (mtp) cc_final: 0.9120 (mtp) REVERT: B 869 MET cc_start: 0.9598 (mtm) cc_final: 0.9099 (mtp) REVERT: B 902 MET cc_start: 0.9871 (mmm) cc_final: 0.9478 (mmp) REVERT: B 1018 ILE cc_start: 0.9841 (mm) cc_final: 0.9578 (tp) REVERT: B 1034 LEU cc_start: 0.9834 (mp) cc_final: 0.9605 (mp) REVERT: B 1062 PHE cc_start: 0.9750 (m-80) cc_final: 0.9442 (m-10) REVERT: D 277 LEU cc_start: 0.9741 (mp) cc_final: 0.9280 (tt) REVERT: D 387 LEU cc_start: 0.8062 (pp) cc_final: 0.7727 (mt) REVERT: D 731 MET cc_start: 0.9207 (ppp) cc_final: 0.8765 (ppp) REVERT: E 104 TRP cc_start: 0.8990 (m100) cc_final: 0.8327 (m100) REVERT: E 568 ASP cc_start: 0.9699 (t0) cc_final: 0.9182 (m-30) REVERT: E 697 MET cc_start: 0.6936 (ptp) cc_final: 0.6480 (ptp) REVERT: E 770 ILE cc_start: 0.9768 (mt) cc_final: 0.9435 (mt) REVERT: E 773 GLU cc_start: 0.9369 (pt0) cc_final: 0.8903 (pp20) REVERT: E 869 MET cc_start: 0.9521 (mtt) cc_final: 0.9172 (mtt) REVERT: E 902 MET cc_start: 0.9732 (mmm) cc_final: 0.9520 (mmm) REVERT: E 1002 GLN cc_start: 0.9425 (tm-30) cc_final: 0.9209 (tm-30) REVERT: E 1029 MET cc_start: 0.9660 (ttt) cc_final: 0.9265 (tpp) REVERT: E 1034 LEU cc_start: 0.9815 (mp) cc_final: 0.9608 (mm) REVERT: G 83 LEU cc_start: 0.9238 (tp) cc_final: 0.8956 (tp) REVERT: I 47 MET cc_start: 0.8550 (mmp) cc_final: 0.8195 (mmm) REVERT: I 69 ASN cc_start: 0.9524 (m-40) cc_final: 0.9303 (t0) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.3770 time to fit residues: 79.3782 Evaluate side-chains 99 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 231 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 265 optimal weight: 0.4980 chunk 215 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN D1002 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 ASN E 955 ASN E 965 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 26130 Z= 0.278 Angle : 0.611 10.466 35551 Z= 0.315 Chirality : 0.043 0.213 4111 Planarity : 0.004 0.088 4571 Dihedral : 5.948 56.493 3949 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.52 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.88 (0.14), residues: 3190 helix: 1.37 (0.20), residues: 673 sheet: -0.71 (0.18), residues: 751 loop : -1.34 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 50 HIS 0.006 0.001 HIS E1048 PHE 0.028 0.002 PHE E 759 TYR 0.022 0.002 TYR G 33 ARG 0.016 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 3.091 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: B 406 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9091 (mp0) REVERT: B 731 MET cc_start: 0.9657 (ptp) cc_final: 0.9452 (ptp) REVERT: B 740 MET cc_start: 0.9329 (mtp) cc_final: 0.9113 (mtp) REVERT: B 869 MET cc_start: 0.9607 (mtm) cc_final: 0.9067 (mtp) REVERT: B 902 MET cc_start: 0.9869 (mmm) cc_final: 0.9472 (mmp) REVERT: B 1018 ILE cc_start: 0.9873 (mm) cc_final: 0.9566 (tp) REVERT: B 1062 PHE cc_start: 0.9758 (m-80) cc_final: 0.9482 (m-80) REVERT: D 277 LEU cc_start: 0.9739 (mp) cc_final: 0.9277 (tt) REVERT: D 387 LEU cc_start: 0.8085 (pp) cc_final: 0.7712 (mt) REVERT: D 731 MET cc_start: 0.9244 (ppp) cc_final: 0.8774 (ppp) REVERT: E 104 TRP cc_start: 0.9131 (m100) cc_final: 0.8381 (m100) REVERT: E 191 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8747 (pm20) REVERT: E 495 TYR cc_start: 0.5337 (m-10) cc_final: 0.5113 (m-10) REVERT: E 869 MET cc_start: 0.9528 (mtt) cc_final: 0.9205 (mtt) REVERT: E 902 MET cc_start: 0.9735 (mmm) cc_final: 0.9435 (mmp) REVERT: E 1029 MET cc_start: 0.9732 (ttt) cc_final: 0.9313 (tpp) REVERT: E 1034 LEU cc_start: 0.9810 (mp) cc_final: 0.9550 (mp) REVERT: G 34 MET cc_start: 0.7529 (tpt) cc_final: 0.7152 (tpt) REVERT: I 62 PHE cc_start: 0.7809 (m-10) cc_final: 0.7558 (m-10) REVERT: I 69 ASN cc_start: 0.9463 (m-40) cc_final: 0.9232 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3618 time to fit residues: 73.0209 Evaluate side-chains 92 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 0.9990 chunk 280 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 311 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26130 Z= 0.192 Angle : 0.550 10.145 35551 Z= 0.283 Chirality : 0.043 0.229 4111 Planarity : 0.004 0.050 4571 Dihedral : 5.733 56.574 3949 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.68 (0.15), residues: 3190 helix: 1.72 (0.21), residues: 674 sheet: -0.63 (0.18), residues: 764 loop : -1.26 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 104 HIS 0.005 0.001 HIS E1048 PHE 0.025 0.001 PHE B 759 TYR 0.011 0.001 TYR G 32 ARG 0.005 0.000 ARG G 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.8882 (ppp) cc_final: 0.8625 (ppp) REVERT: B 731 MET cc_start: 0.9615 (ptp) cc_final: 0.9351 (ptp) REVERT: B 740 MET cc_start: 0.9327 (mtp) cc_final: 0.9105 (mtp) REVERT: B 869 MET cc_start: 0.9594 (mtm) cc_final: 0.9116 (mtp) REVERT: B 902 MET cc_start: 0.9857 (mmm) cc_final: 0.9462 (mmp) REVERT: B 1018 ILE cc_start: 0.9865 (mm) cc_final: 0.9554 (tp) REVERT: B 1062 PHE cc_start: 0.9741 (m-80) cc_final: 0.9375 (m-10) REVERT: D 277 LEU cc_start: 0.9740 (mp) cc_final: 0.9259 (tt) REVERT: D 387 LEU cc_start: 0.8338 (pp) cc_final: 0.8019 (mt) REVERT: D 731 MET cc_start: 0.9221 (ppp) cc_final: 0.8740 (ppp) REVERT: D 742 ILE cc_start: 0.9764 (mt) cc_final: 0.9386 (tp) REVERT: E 104 TRP cc_start: 0.9162 (m100) cc_final: 0.8226 (m100) REVERT: E 191 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8740 (pm20) REVERT: E 495 TYR cc_start: 0.4931 (m-10) cc_final: 0.4708 (m-80) REVERT: E 568 ASP cc_start: 0.9719 (t0) cc_final: 0.9241 (m-30) REVERT: E 697 MET cc_start: 0.6912 (ptp) cc_final: 0.6461 (ptp) REVERT: E 770 ILE cc_start: 0.9768 (mt) cc_final: 0.9450 (mt) REVERT: E 773 GLU cc_start: 0.9302 (pt0) cc_final: 0.8946 (pp20) REVERT: E 869 MET cc_start: 0.9515 (mtt) cc_final: 0.9186 (mtt) REVERT: E 902 MET cc_start: 0.9714 (mmm) cc_final: 0.9383 (mmp) REVERT: E 1029 MET cc_start: 0.9667 (ttt) cc_final: 0.9306 (tpp) REVERT: E 1034 LEU cc_start: 0.9822 (mp) cc_final: 0.9585 (mp) REVERT: G 45 LEU cc_start: 0.4396 (tp) cc_final: 0.4176 (tp) REVERT: G 64 PHE cc_start: 0.7713 (m-80) cc_final: 0.7242 (m-80) REVERT: I 61 ARG cc_start: 0.8224 (mtm110) cc_final: 0.7975 (mtm110) REVERT: I 69 ASN cc_start: 0.9537 (m-40) cc_final: 0.9324 (t0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.3610 time to fit residues: 79.5454 Evaluate side-chains 100 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 177 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 262 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 143 optimal weight: 50.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1048 HIS ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 751 ASN E 784 GLN E 953 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 26130 Z= 0.287 Angle : 0.626 11.195 35551 Z= 0.325 Chirality : 0.044 0.223 4111 Planarity : 0.004 0.083 4571 Dihedral : 6.029 56.911 3949 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.90 (0.15), residues: 3190 helix: 1.40 (0.20), residues: 676 sheet: -0.78 (0.18), residues: 760 loop : -1.33 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 35 HIS 0.008 0.001 HIS I 39 PHE 0.022 0.002 PHE B 759 TYR 0.023 0.002 TYR G 112 ARG 0.005 0.001 ARG G 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 3.321 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: B 697 MET cc_start: 0.8871 (ppp) cc_final: 0.8582 (ppp) REVERT: B 731 MET cc_start: 0.9607 (ptp) cc_final: 0.9298 (ptp) REVERT: B 740 MET cc_start: 0.9326 (mtp) cc_final: 0.9104 (mtp) REVERT: B 869 MET cc_start: 0.9561 (mtm) cc_final: 0.9105 (mtp) REVERT: B 902 MET cc_start: 0.9889 (mmm) cc_final: 0.9505 (mmp) REVERT: B 1062 PHE cc_start: 0.9723 (m-80) cc_final: 0.9343 (m-80) REVERT: D 104 TRP cc_start: 0.9332 (m-90) cc_final: 0.9022 (m-90) REVERT: D 277 LEU cc_start: 0.9741 (mp) cc_final: 0.9262 (tt) REVERT: D 387 LEU cc_start: 0.8761 (pp) cc_final: 0.8203 (mt) REVERT: D 568 ASP cc_start: 0.9364 (t0) cc_final: 0.8936 (p0) REVERT: D 731 MET cc_start: 0.9249 (ppp) cc_final: 0.8741 (ppp) REVERT: D 742 ILE cc_start: 0.9791 (mt) cc_final: 0.9536 (tp) REVERT: E 104 TRP cc_start: 0.9262 (m100) cc_final: 0.8249 (m100) REVERT: E 495 TYR cc_start: 0.5084 (m-10) cc_final: 0.4822 (m-80) REVERT: E 568 ASP cc_start: 0.9711 (t0) cc_final: 0.9263 (m-30) REVERT: E 697 MET cc_start: 0.7225 (ptp) cc_final: 0.6757 (ptp) REVERT: E 869 MET cc_start: 0.9532 (mtt) cc_final: 0.9219 (mtt) REVERT: E 902 MET cc_start: 0.9715 (mmm) cc_final: 0.9406 (mmp) REVERT: E 1062 PHE cc_start: 0.9622 (m-80) cc_final: 0.9414 (m-10) REVERT: G 64 PHE cc_start: 0.7693 (m-80) cc_final: 0.7234 (m-10) REVERT: I 47 MET cc_start: 0.8371 (mmp) cc_final: 0.8078 (mmm) REVERT: I 69 ASN cc_start: 0.9505 (m-40) cc_final: 0.9301 (t0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3796 time to fit residues: 78.1543 Evaluate side-chains 92 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 8.9990 chunk 123 optimal weight: 40.0000 chunk 185 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 26130 Z= 0.374 Angle : 0.721 12.363 35551 Z= 0.377 Chirality : 0.045 0.211 4111 Planarity : 0.005 0.061 4571 Dihedral : 6.626 57.992 3949 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 27.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.49 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.30 (0.14), residues: 3190 helix: 0.88 (0.20), residues: 681 sheet: -1.04 (0.18), residues: 761 loop : -1.51 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 36 HIS 0.009 0.002 HIS D1048 PHE 0.023 0.002 PHE E 338 TYR 0.030 0.002 TYR G 32 ARG 0.008 0.001 ARG G 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.8918 (ppp) cc_final: 0.8632 (ppp) REVERT: B 731 MET cc_start: 0.9579 (ptp) cc_final: 0.9354 (ptp) REVERT: B 740 MET cc_start: 0.9361 (mtp) cc_final: 0.9112 (mtp) REVERT: B 869 MET cc_start: 0.9563 (mtm) cc_final: 0.9064 (mtp) REVERT: B 902 MET cc_start: 0.9890 (mmm) cc_final: 0.9523 (mmp) REVERT: B 1062 PHE cc_start: 0.9688 (m-80) cc_final: 0.9316 (m-80) REVERT: D 104 TRP cc_start: 0.9357 (m-90) cc_final: 0.9017 (m-90) REVERT: D 277 LEU cc_start: 0.9734 (mp) cc_final: 0.9263 (tt) REVERT: D 387 LEU cc_start: 0.8881 (pp) cc_final: 0.8355 (mt) REVERT: D 568 ASP cc_start: 0.9359 (t0) cc_final: 0.8953 (p0) REVERT: D 731 MET cc_start: 0.9219 (ppp) cc_final: 0.8708 (ppp) REVERT: D 742 ILE cc_start: 0.9804 (mt) cc_final: 0.9555 (tp) REVERT: D 759 PHE cc_start: 0.8632 (m-80) cc_final: 0.8387 (m-80) REVERT: E 104 TRP cc_start: 0.9388 (m100) cc_final: 0.8445 (m100) REVERT: E 495 TYR cc_start: 0.5177 (m-10) cc_final: 0.4877 (m-80) REVERT: E 869 MET cc_start: 0.9535 (mtt) cc_final: 0.9197 (mtt) REVERT: E 902 MET cc_start: 0.9717 (mmm) cc_final: 0.9407 (mmp) REVERT: E 1029 MET cc_start: 0.9685 (ttt) cc_final: 0.9475 (ttt) REVERT: E 1062 PHE cc_start: 0.9606 (m-80) cc_final: 0.9400 (m-10) REVERT: G 64 PHE cc_start: 0.7587 (m-80) cc_final: 0.7138 (m-10) REVERT: I 48 ILE cc_start: 0.8490 (mt) cc_final: 0.8027 (tt) REVERT: I 62 PHE cc_start: 0.7685 (m-10) cc_final: 0.7054 (m-10) REVERT: I 69 ASN cc_start: 0.9497 (m-40) cc_final: 0.9279 (t0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3552 time to fit residues: 64.7815 Evaluate side-chains 86 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 289 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 273 optimal weight: 0.9980 chunk 288 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN E 907 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 26130 Z= 0.178 Angle : 0.566 9.799 35551 Z= 0.290 Chirality : 0.044 0.310 4111 Planarity : 0.004 0.055 4571 Dihedral : 5.988 57.886 3949 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.76 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.83 (0.15), residues: 3190 helix: 1.54 (0.21), residues: 686 sheet: -0.84 (0.18), residues: 773 loop : -1.29 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 35 HIS 0.007 0.001 HIS I 39 PHE 0.016 0.001 PHE D 559 TYR 0.011 0.001 TYR D 873 ARG 0.003 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.8984 (ppp) cc_final: 0.8764 (ppp) REVERT: B 740 MET cc_start: 0.9311 (mtp) cc_final: 0.9052 (mtp) REVERT: B 869 MET cc_start: 0.9550 (mtm) cc_final: 0.9075 (mtp) REVERT: B 902 MET cc_start: 0.9855 (mmm) cc_final: 0.9448 (mmp) REVERT: B 1018 ILE cc_start: 0.9853 (mm) cc_final: 0.9513 (tp) REVERT: B 1062 PHE cc_start: 0.9681 (m-80) cc_final: 0.9287 (m-80) REVERT: D 277 LEU cc_start: 0.9718 (mp) cc_final: 0.9192 (tt) REVERT: D 387 LEU cc_start: 0.8847 (pp) cc_final: 0.8399 (mm) REVERT: D 568 ASP cc_start: 0.9368 (t0) cc_final: 0.8985 (p0) REVERT: D 611 LEU cc_start: 0.9542 (tp) cc_final: 0.9299 (tp) REVERT: D 731 MET cc_start: 0.9218 (ppp) cc_final: 0.8679 (ppp) REVERT: D 742 ILE cc_start: 0.9780 (mt) cc_final: 0.9507 (tp) REVERT: D 776 LYS cc_start: 0.9876 (tttt) cc_final: 0.9577 (ptmm) REVERT: E 104 TRP cc_start: 0.9292 (m100) cc_final: 0.8382 (m100) REVERT: E 191 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8735 (pm20) REVERT: E 495 TYR cc_start: 0.4912 (m-10) cc_final: 0.4611 (m-80) REVERT: E 568 ASP cc_start: 0.9701 (t0) cc_final: 0.9264 (m-30) REVERT: E 697 MET cc_start: 0.6962 (ptp) cc_final: 0.6480 (ptp) REVERT: E 770 ILE cc_start: 0.9780 (mt) cc_final: 0.9461 (mt) REVERT: E 773 GLU cc_start: 0.9320 (pt0) cc_final: 0.8844 (pp20) REVERT: E 869 MET cc_start: 0.9499 (mtt) cc_final: 0.9197 (mtt) REVERT: E 902 MET cc_start: 0.9678 (mmm) cc_final: 0.9331 (mmp) REVERT: E 1029 MET cc_start: 0.9653 (ttt) cc_final: 0.9346 (tpp) REVERT: G 64 PHE cc_start: 0.7592 (m-80) cc_final: 0.7152 (m-10) REVERT: I 48 ILE cc_start: 0.8150 (mt) cc_final: 0.7719 (tt) REVERT: I 69 ASN cc_start: 0.9537 (m-40) cc_final: 0.9302 (t0) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.3749 time to fit residues: 76.0659 Evaluate side-chains 95 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 320 optimal weight: 40.0000 chunk 295 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26130 Z= 0.164 Angle : 0.548 9.544 35551 Z= 0.280 Chirality : 0.044 0.229 4111 Planarity : 0.004 0.062 4571 Dihedral : 5.654 56.949 3949 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.62 (0.15), residues: 3190 helix: 1.72 (0.21), residues: 695 sheet: -0.74 (0.18), residues: 784 loop : -1.15 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 104 HIS 0.004 0.001 HIS D1083 PHE 0.018 0.001 PHE D 559 TYR 0.011 0.001 TYR B1067 ARG 0.004 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.942 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: B 731 MET cc_start: 0.9511 (pmm) cc_final: 0.9227 (pmm) REVERT: B 740 MET cc_start: 0.9320 (mtp) cc_final: 0.9075 (mtp) REVERT: B 869 MET cc_start: 0.9563 (mtm) cc_final: 0.9095 (mtp) REVERT: B 902 MET cc_start: 0.9860 (mmm) cc_final: 0.9442 (mmp) REVERT: B 1018 ILE cc_start: 0.9838 (mm) cc_final: 0.9427 (tp) REVERT: B 1062 PHE cc_start: 0.9683 (m-80) cc_final: 0.9272 (m-80) REVERT: D 277 LEU cc_start: 0.9719 (mp) cc_final: 0.9189 (tt) REVERT: D 387 LEU cc_start: 0.8846 (pp) cc_final: 0.8387 (mm) REVERT: D 568 ASP cc_start: 0.9394 (t0) cc_final: 0.9018 (p0) REVERT: D 611 LEU cc_start: 0.9550 (tp) cc_final: 0.9314 (tp) REVERT: D 731 MET cc_start: 0.9225 (ppp) cc_final: 0.8706 (ppp) REVERT: D 742 ILE cc_start: 0.9773 (mt) cc_final: 0.9499 (tp) REVERT: D 776 LYS cc_start: 0.9871 (tttt) cc_final: 0.9583 (ptmm) REVERT: E 104 TRP cc_start: 0.9259 (m100) cc_final: 0.8571 (m100) REVERT: E 191 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8732 (pm20) REVERT: E 495 TYR cc_start: 0.4992 (m-10) cc_final: 0.4694 (m-80) REVERT: E 568 ASP cc_start: 0.9653 (t0) cc_final: 0.9241 (m-30) REVERT: E 697 MET cc_start: 0.7069 (ptp) cc_final: 0.6589 (ptp) REVERT: E 770 ILE cc_start: 0.9773 (mt) cc_final: 0.9473 (mm) REVERT: E 773 GLU cc_start: 0.9329 (pt0) cc_final: 0.8832 (pp20) REVERT: E 869 MET cc_start: 0.9499 (mtt) cc_final: 0.9192 (mtt) REVERT: E 902 MET cc_start: 0.9685 (mmm) cc_final: 0.9336 (mmp) REVERT: E 1062 PHE cc_start: 0.9559 (m-80) cc_final: 0.9335 (m-10) REVERT: G 83 LEU cc_start: 0.8980 (tp) cc_final: 0.8737 (tp) REVERT: I 62 PHE cc_start: 0.7463 (m-10) cc_final: 0.7249 (m-10) REVERT: I 69 ASN cc_start: 0.9494 (m-40) cc_final: 0.9242 (t0) REVERT: I 73 LEU cc_start: 0.7699 (tp) cc_final: 0.7229 (pp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3600 time to fit residues: 72.1345 Evaluate side-chains 97 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 235 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 262 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.054880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.044143 restraints weight = 256527.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.044663 restraints weight = 116056.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.045308 restraints weight = 64473.093| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26130 Z= 0.229 Angle : 0.586 10.653 35551 Z= 0.302 Chirality : 0.043 0.216 4111 Planarity : 0.004 0.063 4571 Dihedral : 5.782 56.650 3949 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.64 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.67 (0.15), residues: 3190 helix: 1.67 (0.21), residues: 692 sheet: -0.77 (0.17), residues: 796 loop : -1.19 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 104 HIS 0.007 0.001 HIS I 39 PHE 0.018 0.001 PHE D 559 TYR 0.014 0.001 TYR G 60 ARG 0.005 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4207.51 seconds wall clock time: 79 minutes 30.56 seconds (4770.56 seconds total)