Starting phenix.real_space_refine on Fri Mar 22 07:14:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uow_26656/03_2024/7uow_26656.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uow_26656/03_2024/7uow_26656.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/7uow_26656/03_2024/7uow_26656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uow_26656/03_2024/7uow_26656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uow_26656/03_2024/7uow_26656.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uow_26656/03_2024/7uow_26656.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= -0.005 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 139 5.16 5 C 20681 2.51 5 N 5377 2.21 5 O 6369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32566 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8483 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 58, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8341 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 57, 'TRANS': 1005} Chain breaks: 7 Chain: "C" Number of atoms: 8516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8516 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "H" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1650 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 11, 'TRANS': 210} Chain: "I" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1634 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain: "J" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1650 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "L" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1634 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "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: "C" 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: 16.87, per 1000 atoms: 0.52 Number of scatterers: 32566 At special positions: 0 Unit cell: (166.78, 159.296, 254.446, 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 139 16.00 O 6369 8.00 N 5377 7.00 C 20681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 343 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A1134 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 709 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 331 " Time building additional restraints: 13.44 Conformation dependent library (CDL) restraints added in 6.1 seconds 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7672 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 71 sheets defined 21.9% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.502A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.744A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.067A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.701A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.530A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 623 removed outlier: 3.686A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.640A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.801A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.679A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.507A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.621A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.582A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1149 removed outlier: 3.685A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.886A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.835A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.935A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.531A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.784A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 631 through 636 removed outlier: 3.696A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 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: 3.517A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 916 through 918 No H-bonds generated for 'chain 'B' and resid 916 through 918' Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.049A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.308A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.827A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1149 removed outlier: 4.311A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.992A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.963A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.980A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 423 Processing helix chain 'C' and resid 616 through 624 removed outlier: 3.711A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Proline residue: C 621 - end of helix removed outlier: 3.890A pdb=" N ILE C 624 " --> pdb=" O PRO C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 624' Processing helix chain 'C' and resid 632 through 636 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.771A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 760 removed outlier: 4.116A pdb=" N PHE C 759 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 778 removed outlier: 3.565A pdb=" N ASN C 777 " --> pdb=" O GLU C 773 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.510A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.544A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.515A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.513A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.013A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 953 " --> pdb=" O GLN C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.536A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.800A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1148 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.926A pdb=" N GLY H 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 131 through 136 removed outlier: 3.572A pdb=" N SER H 134 " --> pdb=" O SER H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 167 removed outlier: 3.633A pdb=" N VAL H 167 " --> pdb=" O THR H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 removed outlier: 3.823A pdb=" N SER H 207 " --> pdb=" O HIS H 204 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN H 208 " --> pdb=" O LYS H 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 204 through 208' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.687A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 60 through 64 removed outlier: 3.802A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'J' and resid 189 through 196 removed outlier: 3.597A pdb=" N GLY J 194 " --> pdb=" O SER J 190 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR J 195 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.644A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 128 removed outlier: 4.136A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 154 Processing helix chain 'L' and resid 184 through 190 removed outlier: 4.065A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 190' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.856A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 4.133A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.172A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.608A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.835A pdb=" N LYS A 310 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY A 601 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.771A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.721A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.845A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.436A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.986A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.669A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.771A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 5.066A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.494A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.928A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU B 276 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.179A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.571A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.967A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.751A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 574 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.584A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.258A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 455 removed outlier: 6.835A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.020A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 719 " --> pdb=" O VAL B1068 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.734A pdb=" N PHE B1121 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS B1083 " --> pdb=" O LYS B1086 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.667A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.132A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.562A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.584A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.600A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 318 removed outlier: 6.236A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 650 " --> pdb=" O PHE C 643 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.944A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.594A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 538 through 541 removed outlier: 3.580A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 13.966A pdb=" N THR C 572 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.764A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.584A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.358A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.648A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS C1083 " --> pdb=" O LYS C1086 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.683A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF3, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.107A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER H 35 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.107A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL H 106 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AF6, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.643A pdb=" N SER H 184 " --> pdb=" O CYS H 144 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL H 146 " --> pdb=" O LEU H 182 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 139 through 141 removed outlier: 3.971A pdb=" N ALA H 140 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 188 " --> pdb=" O ALA H 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'H' and resid 156 through 158 removed outlier: 4.244A pdb=" N SER H 157 " --> pdb=" O ASN H 201 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN H 201 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.653A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 11 through 14 Processing sheet with id=AG2, first strand: chain 'I' and resid 44 through 46 removed outlier: 3.676A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN I 38 " --> pdb=" O ALA I 85 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AG4, first strand: chain 'I' and resid 115 through 119 removed outlier: 3.998A pdb=" N VAL I 134 " --> pdb=" O PHE I 119 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL I 134 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU I 180 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU I 136 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER I 178 " --> pdb=" O LEU I 136 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN I 138 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU I 176 " --> pdb=" O ASN I 138 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N THR I 173 " --> pdb=" O GLN I 167 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN I 167 " --> pdb=" O THR I 173 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER I 175 " --> pdb=" O THR I 165 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 154 through 155 removed outlier: 3.829A pdb=" N ALA I 194 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AG7, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AG8, first strand: chain 'J' and resid 44 through 47 removed outlier: 3.646A pdb=" N GLY J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA J 40 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG J 38 " --> pdb=" O GLU J 46 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 50 through 51 Processing sheet with id=AH1, first strand: chain 'J' and resid 91 through 93 removed outlier: 3.820A pdb=" N ALA J 91 " --> pdb=" O VAL J 113 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL J 113 " --> pdb=" O ALA J 91 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 124 through 128 removed outlier: 3.648A pdb=" N LEU J 145 " --> pdb=" O PHE J 126 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS J 144 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER J 184 " --> pdb=" O CYS J 144 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP J 148 " --> pdb=" O TYR J 180 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR J 180 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 124 through 128 removed outlier: 3.648A pdb=" N LEU J 145 " --> pdb=" O PHE J 126 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS J 144 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER J 184 " --> pdb=" O CYS J 144 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP J 148 " --> pdb=" O TYR J 180 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR J 180 " --> pdb=" O ASP J 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL J 173 " --> pdb=" O SER J 181 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 155 through 157 removed outlier: 3.801A pdb=" N ASN J 203 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER J 157 " --> pdb=" O ASN J 201 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 137 through 140 removed outlier: 5.657A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE L 140 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR L 179 " --> pdb=" O GLN L 161 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 146 through 149 1082 hydrogen bonds defined for protein. 2883 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: 15.01 Time building geometry restraints manager: 14.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5914 1.33 - 1.45: 8803 1.45 - 1.57: 18419 1.57 - 1.69: 1 1.69 - 1.81: 175 Bond restraints: 33312 Sorted by residual: bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.11e+01 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.25e-02 6.40e+03 4.71e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" CB PRO H 151 " pdb=" CG PRO H 151 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 3.99e+00 bond pdb=" C PRO I 95 " pdb=" N PRO I 96 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.91e+00 ... (remaining 33307 not shown) Histogram of bond angle deviations from ideal: 97.41 - 104.75: 620 104.75 - 112.10: 16661 112.10 - 119.44: 10618 119.44 - 126.78: 17044 126.78 - 134.13: 404 Bond angle restraints: 45347 Sorted by residual: angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 111.91 106.64 5.27 8.90e-01 1.26e+00 3.50e+01 angle pdb=" N VAL B1033 " pdb=" CA VAL B1033 " pdb=" C VAL B1033 " ideal model delta sigma weight residual 113.71 108.93 4.78 9.50e-01 1.11e+00 2.53e+01 angle pdb=" C PRO H 151 " pdb=" N GLU H 152 " pdb=" CA GLU H 152 " ideal model delta sigma weight residual 121.62 129.17 -7.55 1.57e+00 4.06e-01 2.31e+01 angle pdb=" N GLN A 954 " pdb=" CA GLN A 954 " pdb=" CB GLN A 954 " ideal model delta sigma weight residual 110.28 117.41 -7.13 1.55e+00 4.16e-01 2.12e+01 angle pdb=" N PRO H 151 " pdb=" CA PRO H 151 " pdb=" C PRO H 151 " ideal model delta sigma weight residual 112.47 121.16 -8.69 2.06e+00 2.36e-01 1.78e+01 ... (remaining 45342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.83: 19045 20.83 - 41.66: 1091 41.66 - 62.49: 183 62.49 - 83.32: 39 83.32 - 104.15: 14 Dihedral angle restraints: 20372 sinusoidal: 8429 harmonic: 11943 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -136.81 50.81 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CA TYR C 904 " pdb=" C TYR C 904 " pdb=" N ARG C 905 " pdb=" CA ARG C 905 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ALA C1070 " pdb=" C ALA C1070 " pdb=" N GLN C1071 " pdb=" CA GLN C1071 " ideal model delta harmonic sigma weight residual -180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 20369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4486 0.066 - 0.132: 754 0.132 - 0.199: 23 0.199 - 0.265: 9 0.265 - 0.331: 4 Chirality restraints: 5276 Sorted by residual: chirality pdb=" CA PRO H 151 " pdb=" N PRO H 151 " pdb=" C PRO H 151 " pdb=" CB PRO H 151 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB ILE B 569 " pdb=" CA ILE B 569 " pdb=" CG1 ILE B 569 " pdb=" CG2 ILE B 569 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 5273 not shown) Planarity restraints: 5832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 150 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO H 151 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO H 151 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO H 151 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE J 150 " -0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO J 151 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO J 151 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO J 151 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.054 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO B 987 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.045 5.00e-02 4.00e+02 ... (remaining 5829 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 674 2.66 - 3.22: 31251 3.22 - 3.78: 48957 3.78 - 4.34: 64414 4.34 - 4.90: 102707 Nonbonded interactions: 248003 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.097 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.099 2.440 nonbonded pdb=" OE1 GLN L 125 " pdb=" OG SER L 132 " model vdw 2.101 2.440 nonbonded pdb=" OG SER L 52 " pdb=" O GLY L 64 " model vdw 2.120 2.440 nonbonded pdb=" OH TYR A 741 " pdb=" O LEU A 962 " model vdw 2.143 2.440 ... (remaining 247998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 1149 or resid 1301 through 1307)) selection = (chain 'B' and (resid 14 through 542 or resid 544 through 623 or resid 633 throu \ gh 1149 or resid 1301 through 1307)) selection = (chain 'C' and (resid 14 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 542 or resid 544 through 623 or resid 633 through 11 \ 49 or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 19.160 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 86.570 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 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 0.100 33312 Z= 0.216 Angle : 0.639 11.855 45347 Z= 0.335 Chirality : 0.047 0.331 5276 Planarity : 0.005 0.119 5797 Dihedral : 13.683 104.149 12694 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 0.14 % Allowed : 0.17 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 4063 helix: 0.86 (0.20), residues: 697 sheet: -0.65 (0.17), residues: 975 loop : -1.23 (0.13), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP I 35 HIS 0.009 0.001 HIS H 204 PHE 0.022 0.001 PHE B 275 TYR 0.021 0.001 TYR C 904 ARG 0.007 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 446 time to evaluate : 3.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8599 (m110) cc_final: 0.7756 (t0) REVERT: A 293 LEU cc_start: 0.7674 (tt) cc_final: 0.7403 (tt) REVERT: A 386 LYS cc_start: 0.9145 (tptt) cc_final: 0.8751 (pttt) REVERT: A 387 LEU cc_start: 0.7826 (mt) cc_final: 0.7261 (mt) REVERT: A 563 GLN cc_start: 0.7635 (mt0) cc_final: 0.7354 (mt0) REVERT: A 584 ILE cc_start: 0.9252 (mp) cc_final: 0.9046 (mm) REVERT: A 586 ASP cc_start: 0.7993 (m-30) cc_final: 0.7702 (m-30) REVERT: A 755 GLN cc_start: 0.8850 (mt0) cc_final: 0.8567 (mm-40) REVERT: A 900 MET cc_start: 0.7822 (mmt) cc_final: 0.7303 (mmm) REVERT: A 973 ILE cc_start: 0.9063 (pt) cc_final: 0.8835 (tt) REVERT: A 981 LEU cc_start: 0.8883 (pp) cc_final: 0.8261 (tp) REVERT: A 1082 CYS cc_start: 0.6124 (t) cc_final: 0.5876 (t) REVERT: B 121 ASN cc_start: 0.8451 (m110) cc_final: 0.8218 (p0) REVERT: B 135 PHE cc_start: 0.7822 (m-80) cc_final: 0.7569 (m-80) REVERT: B 297 SER cc_start: 0.9318 (m) cc_final: 0.8918 (p) REVERT: B 386 LYS cc_start: 0.8060 (mttt) cc_final: 0.7093 (tttt) REVERT: B 695 TYR cc_start: 0.9274 (p90) cc_final: 0.8792 (p90) REVERT: B 775 ASP cc_start: 0.8090 (m-30) cc_final: 0.7869 (m-30) REVERT: B 894 LEU cc_start: 0.9567 (mt) cc_final: 0.9252 (mt) REVERT: B 900 MET cc_start: 0.8120 (ttm) cc_final: 0.7895 (tpt) REVERT: C 140 PHE cc_start: 0.6884 (p90) cc_final: 0.6449 (p90) REVERT: C 211 ASN cc_start: 0.8839 (p0) cc_final: 0.8503 (m-40) REVERT: C 221 SER cc_start: 0.8755 (m) cc_final: 0.8536 (p) REVERT: C 242 LEU cc_start: 0.9010 (mm) cc_final: 0.8791 (mm) REVERT: C 582 LEU cc_start: 0.8989 (mp) cc_final: 0.8631 (tt) REVERT: C 614 ASP cc_start: 0.8146 (t0) cc_final: 0.7864 (t70) REVERT: C 699 LEU cc_start: 0.8959 (mm) cc_final: 0.8689 (mm) REVERT: C 970 PHE cc_start: 0.9002 (m-10) cc_final: 0.8604 (m-80) REVERT: H 34 MET cc_start: -0.0094 (ttt) cc_final: -0.1913 (ptp) REVERT: H 104 MET cc_start: 0.0605 (ppp) cc_final: 0.0287 (pmm) REVERT: L 155 LEU cc_start: 0.5202 (tp) cc_final: 0.4846 (tt) outliers start: 5 outliers final: 2 residues processed: 449 average time/residue: 0.4326 time to fit residues: 319.2386 Evaluate side-chains 236 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 165 optimal weight: 0.0670 chunk 319 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 370 optimal weight: 0.0170 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 207 HIS A 211 ASN A 544 ASN A 580 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN A1005 GLN B 99 ASN ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 784 GLN B 965 GLN B1048 HIS ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 245 HIS C 314 GLN C 613 GLN C 764 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 907 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1083 HIS C1088 HIS C1119 ASN H 32 ASN H 76 ASN I 90 GLN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 HIS L 6 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 33312 Z= 0.218 Angle : 0.608 10.351 45347 Z= 0.317 Chirality : 0.047 0.334 5276 Planarity : 0.005 0.120 5797 Dihedral : 7.902 80.430 5399 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.80 % Favored : 95.10 % Rotamer: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4063 helix: 0.88 (0.20), residues: 724 sheet: -0.58 (0.17), residues: 972 loop : -1.19 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 35 HIS 0.005 0.001 HIS C 66 PHE 0.023 0.001 PHE C 906 TYR 0.022 0.001 TYR C 904 ARG 0.016 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 317 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8807 (m-40) cc_final: 0.7679 (p0) REVERT: A 386 LYS cc_start: 0.9090 (tptt) cc_final: 0.8786 (pttt) REVERT: A 387 LEU cc_start: 0.8140 (mt) cc_final: 0.7679 (mt) REVERT: A 586 ASP cc_start: 0.7964 (m-30) cc_final: 0.7650 (m-30) REVERT: A 755 GLN cc_start: 0.8943 (mt0) cc_final: 0.8342 (mm-40) REVERT: A 900 MET cc_start: 0.8120 (mmt) cc_final: 0.7501 (mmt) REVERT: A 981 LEU cc_start: 0.8812 (pp) cc_final: 0.8443 (tp) REVERT: B 135 PHE cc_start: 0.7763 (m-80) cc_final: 0.7468 (m-10) REVERT: B 293 LEU cc_start: 0.9176 (tt) cc_final: 0.8845 (mm) REVERT: B 386 LYS cc_start: 0.8338 (mttt) cc_final: 0.7268 (tttt) REVERT: B 695 TYR cc_start: 0.9376 (p90) cc_final: 0.8849 (p90) REVERT: B 894 LEU cc_start: 0.9574 (mt) cc_final: 0.9238 (mt) REVERT: B 900 MET cc_start: 0.8167 (ttm) cc_final: 0.7933 (tpt) REVERT: C 140 PHE cc_start: 0.7158 (p90) cc_final: 0.6503 (p90) REVERT: C 196 ASN cc_start: 0.7405 (t0) cc_final: 0.6674 (p0) REVERT: C 211 ASN cc_start: 0.8802 (p0) cc_final: 0.8520 (m-40) REVERT: C 212 LEU cc_start: 0.7836 (tp) cc_final: 0.7542 (tt) REVERT: C 221 SER cc_start: 0.8736 (m) cc_final: 0.8471 (p) REVERT: C 439 ASN cc_start: 0.9004 (t0) cc_final: 0.8774 (m-40) REVERT: C 614 ASP cc_start: 0.8208 (t0) cc_final: 0.7815 (t70) REVERT: C 699 LEU cc_start: 0.8930 (mm) cc_final: 0.8676 (mm) REVERT: C 803 SER cc_start: 0.8725 (p) cc_final: 0.8226 (t) REVERT: H 34 MET cc_start: 0.0449 (ttt) cc_final: -0.1155 (ptp) REVERT: H 104 MET cc_start: 0.0505 (ppp) cc_final: 0.0081 (mtm) REVERT: J 82 MET cc_start: 0.0694 (mtm) cc_final: 0.0291 (mtm) REVERT: L 155 LEU cc_start: 0.5150 (tp) cc_final: 0.4823 (tt) outliers start: 4 outliers final: 1 residues processed: 321 average time/residue: 0.3810 time to fit residues: 211.1414 Evaluate side-chains 212 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 308 optimal weight: 2.9990 chunk 252 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 20.0000 chunk 330 optimal weight: 30.0000 chunk 368 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 297 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 134 GLN B 149 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 314 GLN C 414 GLN C 658 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 90 GLN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 33312 Z= 0.448 Angle : 0.738 12.410 45347 Z= 0.384 Chirality : 0.049 0.331 5276 Planarity : 0.006 0.121 5797 Dihedral : 7.721 76.718 5399 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.97 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 4063 helix: 0.41 (0.19), residues: 729 sheet: -0.74 (0.16), residues: 1007 loop : -1.42 (0.13), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 104 HIS 0.009 0.002 HIS C1048 PHE 0.027 0.003 PHE C 906 TYR 0.037 0.002 TYR C 904 ARG 0.010 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 3.693 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: A 198 ASP cc_start: 0.8303 (m-30) cc_final: 0.7904 (p0) REVERT: A 386 LYS cc_start: 0.9070 (tptt) cc_final: 0.8769 (pttt) REVERT: A 586 ASP cc_start: 0.7901 (m-30) cc_final: 0.7616 (m-30) REVERT: A 904 TYR cc_start: 0.7521 (t80) cc_final: 0.7309 (t80) REVERT: A 965 GLN cc_start: 0.9088 (tp40) cc_final: 0.8413 (tp-100) REVERT: A 968 SER cc_start: 0.9165 (t) cc_final: 0.8922 (t) REVERT: A 981 LEU cc_start: 0.8868 (pp) cc_final: 0.8370 (tp) REVERT: B 133 PHE cc_start: 0.8386 (m-10) cc_final: 0.8127 (m-80) REVERT: B 135 PHE cc_start: 0.7951 (m-80) cc_final: 0.7553 (m-10) REVERT: B 386 LYS cc_start: 0.8367 (mttt) cc_final: 0.7350 (tttt) REVERT: B 695 TYR cc_start: 0.9533 (p90) cc_final: 0.8968 (p90) REVERT: B 900 MET cc_start: 0.8422 (ttm) cc_final: 0.8010 (tpt) REVERT: C 140 PHE cc_start: 0.7192 (p90) cc_final: 0.6511 (p90) REVERT: C 211 ASN cc_start: 0.8661 (p0) cc_final: 0.8430 (m-40) REVERT: C 221 SER cc_start: 0.8885 (m) cc_final: 0.8496 (p) REVERT: C 439 ASN cc_start: 0.9010 (t0) cc_final: 0.8763 (m-40) REVERT: C 614 ASP cc_start: 0.8162 (t0) cc_final: 0.7825 (t70) REVERT: C 699 LEU cc_start: 0.8923 (mm) cc_final: 0.8603 (mm) REVERT: C 803 SER cc_start: 0.8977 (p) cc_final: 0.8517 (t) REVERT: C 900 MET cc_start: 0.9146 (mtm) cc_final: 0.8805 (mtm) REVERT: C 969 ASN cc_start: 0.9458 (p0) cc_final: 0.9182 (p0) REVERT: H 34 MET cc_start: 0.0283 (ttt) cc_final: -0.0593 (ptp) REVERT: J 82 MET cc_start: 0.0563 (mtm) cc_final: -0.0419 (mtm) REVERT: J 104 MET cc_start: -0.0367 (mmp) cc_final: -0.1373 (tpp) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.4007 time to fit residues: 182.7874 Evaluate side-chains 179 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 20.0000 chunk 279 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 249 optimal weight: 4.9990 chunk 372 optimal weight: 20.0000 chunk 394 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 353 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 926 GLN A1005 GLN B 121 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 33312 Z= 0.322 Angle : 0.643 10.065 45347 Z= 0.333 Chirality : 0.048 0.323 5276 Planarity : 0.005 0.122 5797 Dihedral : 7.296 77.079 5399 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4063 helix: 0.52 (0.19), residues: 730 sheet: -0.68 (0.16), residues: 972 loop : -1.39 (0.13), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 633 HIS 0.007 0.001 HIS C1048 PHE 0.026 0.002 PHE B 275 TYR 0.027 0.001 TYR C 904 ARG 0.005 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 3.955 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: A 135 PHE cc_start: 0.8353 (m-80) cc_final: 0.8029 (m-80) REVERT: A 386 LYS cc_start: 0.9039 (tptt) cc_final: 0.8754 (pttt) REVERT: A 584 ILE cc_start: 0.9303 (mm) cc_final: 0.9101 (mm) REVERT: A 586 ASP cc_start: 0.7894 (m-30) cc_final: 0.7571 (m-30) REVERT: A 697 MET cc_start: 0.8827 (tpt) cc_final: 0.8252 (tpt) REVERT: A 965 GLN cc_start: 0.9076 (tp40) cc_final: 0.8248 (tp-100) REVERT: A 968 SER cc_start: 0.9087 (t) cc_final: 0.8761 (t) REVERT: B 121 ASN cc_start: 0.8685 (m-40) cc_final: 0.8199 (p0) REVERT: B 135 PHE cc_start: 0.7852 (m-80) cc_final: 0.7502 (m-10) REVERT: B 386 LYS cc_start: 0.8351 (mttt) cc_final: 0.7243 (tttt) REVERT: B 695 TYR cc_start: 0.9480 (p90) cc_final: 0.9097 (p90) REVERT: B 900 MET cc_start: 0.8333 (ttm) cc_final: 0.7479 (tmm) REVERT: C 177 MET cc_start: 0.6158 (mmt) cc_final: 0.5739 (mmm) REVERT: C 211 ASN cc_start: 0.8667 (p0) cc_final: 0.8414 (m-40) REVERT: C 212 LEU cc_start: 0.8003 (tp) cc_final: 0.7725 (tt) REVERT: C 671 CYS cc_start: 0.6601 (m) cc_final: 0.5292 (m) REVERT: C 699 LEU cc_start: 0.8986 (mm) cc_final: 0.8539 (mm) REVERT: C 803 SER cc_start: 0.8979 (p) cc_final: 0.8443 (t) REVERT: C 969 ASN cc_start: 0.9445 (p0) cc_final: 0.9209 (p0) REVERT: H 34 MET cc_start: 0.0209 (ttt) cc_final: -0.0577 (ptp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.4060 time to fit residues: 182.0223 Evaluate side-chains 173 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 4.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 20.0000 chunk 223 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 293 optimal weight: 0.0370 chunk 162 optimal weight: 8.9990 chunk 336 optimal weight: 9.9990 chunk 272 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 5.9990 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 658 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 33312 Z= 0.297 Angle : 0.624 10.019 45347 Z= 0.324 Chirality : 0.047 0.318 5276 Planarity : 0.005 0.125 5797 Dihedral : 7.130 78.200 5399 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 4063 helix: 0.66 (0.20), residues: 724 sheet: -0.70 (0.16), residues: 982 loop : -1.41 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 107 HIS 0.008 0.001 HIS C1048 PHE 0.023 0.002 PHE B 275 TYR 0.043 0.001 TYR L 87 ARG 0.010 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8184 (mmp80) cc_final: 0.7973 (mmp80) REVERT: A 100 ILE cc_start: 0.9181 (pt) cc_final: 0.8946 (mt) REVERT: A 135 PHE cc_start: 0.8180 (m-80) cc_final: 0.7771 (m-80) REVERT: A 386 LYS cc_start: 0.9021 (tptt) cc_final: 0.8746 (pttt) REVERT: A 586 ASP cc_start: 0.7875 (m-30) cc_final: 0.7554 (m-30) REVERT: A 697 MET cc_start: 0.8822 (tpt) cc_final: 0.8277 (tpt) REVERT: A 904 TYR cc_start: 0.7258 (t80) cc_final: 0.6837 (t80) REVERT: A 965 GLN cc_start: 0.9088 (tp40) cc_final: 0.8277 (tp-100) REVERT: A 988 GLU cc_start: 0.8257 (tm-30) cc_final: 0.8040 (tm-30) REVERT: B 121 ASN cc_start: 0.8434 (m-40) cc_final: 0.8206 (p0) REVERT: B 135 PHE cc_start: 0.8007 (m-80) cc_final: 0.7307 (m-10) REVERT: B 238 PHE cc_start: 0.7685 (p90) cc_final: 0.7451 (p90) REVERT: B 386 LYS cc_start: 0.8370 (mttt) cc_final: 0.7152 (tttt) REVERT: B 695 TYR cc_start: 0.9502 (p90) cc_final: 0.9089 (p90) REVERT: B 900 MET cc_start: 0.8305 (ttm) cc_final: 0.7492 (tmm) REVERT: C 177 MET cc_start: 0.6165 (mmt) cc_final: 0.5923 (mmm) REVERT: C 211 ASN cc_start: 0.8675 (p0) cc_final: 0.8407 (m-40) REVERT: C 212 LEU cc_start: 0.8033 (tp) cc_final: 0.7708 (tt) REVERT: C 803 SER cc_start: 0.9015 (p) cc_final: 0.8508 (t) REVERT: C 900 MET cc_start: 0.8687 (mtm) cc_final: 0.8357 (mtt) REVERT: C 969 ASN cc_start: 0.9439 (p0) cc_final: 0.9234 (p0) REVERT: H 34 MET cc_start: 0.0447 (ttt) cc_final: -0.0208 (ptp) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.3894 time to fit residues: 169.1626 Evaluate side-chains 173 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 6.9990 chunk 355 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 394 optimal weight: 40.0000 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 218 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 487 ASN C 658 ASN C 751 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN J 208 ASN L 148 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 33312 Z= 0.587 Angle : 0.866 14.761 45347 Z= 0.451 Chirality : 0.053 0.325 5276 Planarity : 0.006 0.123 5797 Dihedral : 8.007 77.994 5399 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.08 % Favored : 90.79 % Rotamer: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.12), residues: 4063 helix: -0.60 (0.18), residues: 746 sheet: -0.84 (0.16), residues: 981 loop : -1.79 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 886 HIS 0.017 0.003 HIS C1048 PHE 0.036 0.003 PHE B 58 TYR 0.036 0.002 TYR B 873 ARG 0.016 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8129 (mmp80) cc_final: 0.7286 (mpp-170) REVERT: A 30 ASN cc_start: 0.8721 (p0) cc_final: 0.8519 (p0) REVERT: A 100 ILE cc_start: 0.9243 (pt) cc_final: 0.9019 (mt) REVERT: A 135 PHE cc_start: 0.8309 (m-80) cc_final: 0.8034 (m-80) REVERT: A 140 PHE cc_start: 0.8218 (p90) cc_final: 0.7991 (p90) REVERT: A 586 ASP cc_start: 0.7831 (m-30) cc_final: 0.7567 (m-30) REVERT: A 904 TYR cc_start: 0.7795 (t80) cc_final: 0.7377 (t80) REVERT: B 121 ASN cc_start: 0.8352 (m-40) cc_final: 0.8141 (p0) REVERT: B 135 PHE cc_start: 0.8246 (m-80) cc_final: 0.7546 (m-10) REVERT: B 238 PHE cc_start: 0.7943 (p90) cc_final: 0.7698 (p90) REVERT: B 386 LYS cc_start: 0.8579 (mttt) cc_final: 0.7330 (tttt) REVERT: B 695 TYR cc_start: 0.9519 (p90) cc_final: 0.9234 (p90) REVERT: C 177 MET cc_start: 0.5950 (mmt) cc_final: 0.5705 (mmm) REVERT: C 211 ASN cc_start: 0.8718 (p0) cc_final: 0.8405 (m-40) REVERT: C 212 LEU cc_start: 0.8252 (tp) cc_final: 0.7931 (tt) REVERT: C 519 HIS cc_start: 0.7936 (p90) cc_final: 0.7695 (p90) REVERT: C 803 SER cc_start: 0.9232 (p) cc_final: 0.8778 (t) REVERT: C 900 MET cc_start: 0.9054 (mtm) cc_final: 0.8798 (mtm) REVERT: H 34 MET cc_start: 0.0175 (ttt) cc_final: -0.0380 (ptp) REVERT: J 74 SER cc_start: 0.6630 (p) cc_final: 0.6299 (m) outliers start: 2 outliers final: 1 residues processed: 226 average time/residue: 0.3952 time to fit residues: 152.9070 Evaluate side-chains 150 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 50.0000 chunk 44 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 288 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 332 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 393 optimal weight: 50.0000 chunk 246 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 245 HIS C 658 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 33312 Z= 0.267 Angle : 0.637 10.154 45347 Z= 0.329 Chirality : 0.048 0.315 5276 Planarity : 0.005 0.125 5797 Dihedral : 7.296 78.470 5399 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.13), residues: 4063 helix: 0.27 (0.19), residues: 719 sheet: -0.80 (0.16), residues: 989 loop : -1.54 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 64 HIS 0.017 0.001 HIS C 207 PHE 0.026 0.002 PHE B 275 TYR 0.029 0.002 TYR C 904 ARG 0.007 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 3.940 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: A 21 ARG cc_start: 0.8118 (mmp80) cc_final: 0.7316 (mpp-170) REVERT: A 100 ILE cc_start: 0.9216 (pt) cc_final: 0.8758 (mt) REVERT: A 135 PHE cc_start: 0.8340 (m-80) cc_final: 0.8064 (m-80) REVERT: A 140 PHE cc_start: 0.8168 (p90) cc_final: 0.7880 (p90) REVERT: A 386 LYS cc_start: 0.8942 (tptt) cc_final: 0.8696 (pttt) REVERT: A 586 ASP cc_start: 0.7880 (m-30) cc_final: 0.7585 (m-30) REVERT: A 697 MET cc_start: 0.8812 (tpt) cc_final: 0.8321 (tpt) REVERT: A 904 TYR cc_start: 0.7404 (t80) cc_final: 0.7147 (t80) REVERT: A 981 LEU cc_start: 0.8686 (pp) cc_final: 0.8292 (tp) REVERT: B 135 PHE cc_start: 0.7997 (m-80) cc_final: 0.7270 (m-10) REVERT: B 223 LEU cc_start: 0.9235 (mt) cc_final: 0.9010 (mt) REVERT: B 238 PHE cc_start: 0.7788 (p90) cc_final: 0.7510 (p90) REVERT: B 242 LEU cc_start: 0.8350 (mm) cc_final: 0.8077 (mt) REVERT: B 386 LYS cc_start: 0.8512 (mttt) cc_final: 0.7222 (tttt) REVERT: B 712 ILE cc_start: 0.8908 (tp) cc_final: 0.8671 (tp) REVERT: C 211 ASN cc_start: 0.8815 (p0) cc_final: 0.8497 (m-40) REVERT: C 212 LEU cc_start: 0.8169 (tp) cc_final: 0.7819 (tt) REVERT: C 238 PHE cc_start: 0.8401 (p90) cc_final: 0.8146 (p90) REVERT: C 671 CYS cc_start: 0.6337 (m) cc_final: 0.5178 (m) REVERT: C 697 MET cc_start: 0.8273 (tpt) cc_final: 0.8010 (tpt) REVERT: C 900 MET cc_start: 0.8998 (mtm) cc_final: 0.8763 (mtm) REVERT: H 34 MET cc_start: 0.0320 (ttt) cc_final: -0.0234 (ptm) REVERT: J 74 SER cc_start: 0.6468 (p) cc_final: 0.6111 (m) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3875 time to fit residues: 164.1361 Evaluate side-chains 175 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 4.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 234 optimal weight: 0.2980 chunk 118 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 309 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 33312 Z= 0.244 Angle : 0.615 10.089 45347 Z= 0.315 Chirality : 0.047 0.315 5276 Planarity : 0.005 0.126 5797 Dihedral : 7.002 78.707 5399 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 4063 helix: 0.52 (0.20), residues: 729 sheet: -0.67 (0.16), residues: 967 loop : -1.48 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.008 0.001 HIS C 207 PHE 0.024 0.002 PHE B 275 TYR 0.030 0.001 TYR C 904 ARG 0.011 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8108 (mmp80) cc_final: 0.7352 (mpp-170) REVERT: A 100 ILE cc_start: 0.9121 (pt) cc_final: 0.8815 (mt) REVERT: A 135 PHE cc_start: 0.8385 (m-80) cc_final: 0.8152 (m-80) REVERT: A 140 PHE cc_start: 0.8201 (p90) cc_final: 0.7874 (p90) REVERT: A 144 TYR cc_start: 0.3602 (p90) cc_final: 0.3106 (p90) REVERT: A 386 LYS cc_start: 0.8965 (tptt) cc_final: 0.8726 (pttt) REVERT: A 697 MET cc_start: 0.8826 (tpt) cc_final: 0.8316 (tpt) REVERT: A 904 TYR cc_start: 0.7376 (t80) cc_final: 0.7075 (t80) REVERT: A 981 LEU cc_start: 0.8659 (pp) cc_final: 0.8264 (tp) REVERT: A 988 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 1048 HIS cc_start: 0.8680 (t-170) cc_final: 0.8447 (t-170) REVERT: B 135 PHE cc_start: 0.8038 (m-80) cc_final: 0.7635 (m-10) REVERT: B 238 PHE cc_start: 0.7751 (p90) cc_final: 0.7418 (p90) REVERT: B 242 LEU cc_start: 0.8342 (mm) cc_final: 0.7998 (mt) REVERT: B 386 LYS cc_start: 0.8489 (mttt) cc_final: 0.7225 (tttt) REVERT: C 121 ASN cc_start: 0.7395 (m-40) cc_final: 0.6405 (p0) REVERT: C 211 ASN cc_start: 0.8794 (p0) cc_final: 0.8501 (m-40) REVERT: C 212 LEU cc_start: 0.8173 (tp) cc_final: 0.7814 (tt) REVERT: C 238 PHE cc_start: 0.8380 (p90) cc_final: 0.8083 (p90) REVERT: C 585 LEU cc_start: 0.9252 (mm) cc_final: 0.8931 (mp) REVERT: C 803 SER cc_start: 0.9015 (p) cc_final: 0.8440 (t) REVERT: C 900 MET cc_start: 0.8972 (mtm) cc_final: 0.8649 (mtm) REVERT: H 34 MET cc_start: 0.0369 (ttt) cc_final: -0.0116 (ptm) REVERT: J 74 SER cc_start: 0.6427 (p) cc_final: 0.6086 (m) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.4117 time to fit residues: 172.9094 Evaluate side-chains 181 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 50.0000 chunk 376 optimal weight: 50.0000 chunk 343 optimal weight: 6.9990 chunk 366 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 287 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 331 optimal weight: 40.0000 chunk 346 optimal weight: 9.9990 chunk 365 optimal weight: 0.7980 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 544 ASN C 658 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 33312 Z= 0.506 Angle : 0.793 12.210 45347 Z= 0.410 Chirality : 0.052 0.326 5276 Planarity : 0.006 0.125 5797 Dihedral : 7.658 78.894 5399 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.57 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 4063 helix: -0.22 (0.18), residues: 748 sheet: -0.74 (0.17), residues: 925 loop : -1.72 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 64 HIS 0.013 0.002 HIS C1048 PHE 0.029 0.003 PHE B 970 TYR 0.037 0.002 TYR B 873 ARG 0.010 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8808 (m-40) cc_final: 0.7380 (p0) REVERT: A 135 PHE cc_start: 0.8367 (m-80) cc_final: 0.8150 (m-80) REVERT: A 140 PHE cc_start: 0.8200 (p90) cc_final: 0.7869 (p90) REVERT: A 904 TYR cc_start: 0.7645 (t80) cc_final: 0.7340 (t80) REVERT: A 981 LEU cc_start: 0.8755 (pp) cc_final: 0.8341 (tp) REVERT: B 386 LYS cc_start: 0.8554 (mttt) cc_final: 0.7259 (tttt) REVERT: B 712 ILE cc_start: 0.8930 (tp) cc_final: 0.8682 (tp) REVERT: C 106 PHE cc_start: 0.8565 (m-10) cc_final: 0.8296 (m-10) REVERT: C 121 ASN cc_start: 0.7253 (m-40) cc_final: 0.6237 (p0) REVERT: C 211 ASN cc_start: 0.8803 (p0) cc_final: 0.8469 (m-40) REVERT: C 212 LEU cc_start: 0.8304 (tp) cc_final: 0.7984 (tt) REVERT: C 238 PHE cc_start: 0.8453 (p90) cc_final: 0.8201 (p90) REVERT: C 276 LEU cc_start: 0.8150 (tp) cc_final: 0.7929 (tp) REVERT: C 671 CYS cc_start: 0.6873 (m) cc_final: 0.6050 (m) REVERT: H 34 MET cc_start: 0.0177 (ttt) cc_final: -0.0067 (ptm) REVERT: J 74 SER cc_start: 0.6636 (p) cc_final: 0.6216 (m) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.4276 time to fit residues: 161.6777 Evaluate side-chains 153 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 3.9990 chunk 387 optimal weight: 30.0000 chunk 236 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 269 optimal weight: 8.9990 chunk 406 optimal weight: 6.9990 chunk 374 optimal weight: 30.0000 chunk 323 optimal weight: 0.5980 chunk 33 optimal weight: 20.0000 chunk 250 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 658 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 GLN ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 33312 Z= 0.260 Angle : 0.642 10.900 45347 Z= 0.329 Chirality : 0.048 0.314 5276 Planarity : 0.005 0.126 5797 Dihedral : 7.180 78.930 5399 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 4063 helix: 0.37 (0.19), residues: 727 sheet: -0.66 (0.17), residues: 910 loop : -1.58 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 633 HIS 0.006 0.001 HIS C 207 PHE 0.024 0.002 PHE B 275 TYR 0.029 0.001 TYR C 904 ARG 0.007 0.000 ARG C 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8289 (mt) cc_final: 0.8019 (mm) REVERT: A 135 PHE cc_start: 0.8337 (m-80) cc_final: 0.7771 (m-80) REVERT: A 140 PHE cc_start: 0.8193 (p90) cc_final: 0.7902 (p90) REVERT: A 697 MET cc_start: 0.8850 (tpt) cc_final: 0.8409 (tpt) REVERT: A 981 LEU cc_start: 0.8651 (pp) cc_final: 0.8269 (tp) REVERT: A 1048 HIS cc_start: 0.8713 (t-170) cc_final: 0.8506 (t-170) REVERT: B 238 PHE cc_start: 0.7780 (p90) cc_final: 0.7417 (p90) REVERT: B 242 LEU cc_start: 0.8451 (mm) cc_final: 0.8116 (mt) REVERT: B 386 LYS cc_start: 0.8392 (mttt) cc_final: 0.7142 (mttt) REVERT: B 969 ASN cc_start: 0.8947 (p0) cc_final: 0.8683 (p0) REVERT: C 106 PHE cc_start: 0.8417 (m-10) cc_final: 0.8151 (m-10) REVERT: C 121 ASN cc_start: 0.7224 (m-40) cc_final: 0.6044 (p0) REVERT: C 211 ASN cc_start: 0.8760 (p0) cc_final: 0.8447 (m-40) REVERT: C 212 LEU cc_start: 0.8364 (tp) cc_final: 0.8023 (tt) REVERT: C 238 PHE cc_start: 0.8231 (p90) cc_final: 0.7958 (p90) REVERT: C 585 LEU cc_start: 0.9262 (mm) cc_final: 0.8941 (mp) REVERT: C 900 MET cc_start: 0.9021 (mtm) cc_final: 0.8643 (mtm) REVERT: H 34 MET cc_start: 0.0100 (ttt) cc_final: -0.0105 (ptm) REVERT: J 74 SER cc_start: 0.6593 (p) cc_final: 0.6149 (m) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.4003 time to fit residues: 164.1679 Evaluate side-chains 179 residues out of total 3585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 chunk 47 optimal weight: 30.0000 chunk 89 optimal weight: 3.9990 chunk 324 optimal weight: 50.0000 chunk 135 optimal weight: 3.9990 chunk 332 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 658 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.118897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080137 restraints weight = 107402.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.075397 restraints weight = 86846.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076237 restraints weight = 85932.922| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 33312 Z= 0.352 Angle : 0.686 10.213 45347 Z= 0.353 Chirality : 0.049 0.314 5276 Planarity : 0.005 0.126 5797 Dihedral : 7.311 78.992 5399 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.85 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 4063 helix: 0.25 (0.19), residues: 729 sheet: -0.68 (0.17), residues: 917 loop : -1.65 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 886 HIS 0.008 0.002 HIS C1048 PHE 0.027 0.002 PHE B 275 TYR 0.052 0.002 TYR J 102 ARG 0.007 0.001 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5503.52 seconds wall clock time: 103 minutes 3.12 seconds (6183.12 seconds total)