Starting phenix.real_space_refine on Fri Dec 15 07:32:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/12_2023/7uz9_26883.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/12_2023/7uz9_26883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/12_2023/7uz9_26883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/12_2023/7uz9_26883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/12_2023/7uz9_26883.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/12_2023/7uz9_26883.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 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 132 5.16 5 C 19515 2.51 5 N 5040 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30669 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 961 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "M" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 961 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "P" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 961 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "Q" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 16.06, per 1000 atoms: 0.52 Number of scatterers: 30669 At special positions: 0 Unit cell: (158.08, 178.88, 196.352, 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 132 16.00 O 5982 8.00 N 5040 7.00 C 19515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 61 " " NAG A1313 " - " ASN A 122 " " NAG A1314 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 61 " " NAG B1313 " - " ASN B 122 " " NAG B1314 " - " ASN B 282 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C 61 " " NAG C1313 " - " ASN C 122 " " NAG C1314 " - " ASN C 282 " Time building additional restraints: 12.13 Conformation dependent library (CDL) restraints added in 5.7 seconds 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 65 sheets defined 22.1% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.505A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 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 885 through 890 removed outlier: 4.091A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.716A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.599A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (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 1141 through 1147 removed outlier: 3.751A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1147' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.898A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) 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 897 through 908 removed outlier: 3.952A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.997A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 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 967 removed outlier: 3.603A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.165A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.982A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (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 1141 through 1147 removed outlier: 3.650A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1147' Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.634A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.703A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.616A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.640A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.574A pdb=" N SER C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.730A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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: 3.732A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.216A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (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 1147 removed outlier: 3.529A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1147' Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.560A pdb=" N SER H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 removed outlier: 3.813A pdb=" N VAL L 99 " --> pdb=" O ALA L 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 37 Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'N' and resid 95 through 99 removed outlier: 3.707A pdb=" N VAL N 99 " --> pdb=" O ALA N 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.648A pdb=" N TYR P 37 " --> pdb=" O PHE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 99 Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.790A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.134A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 5.660A 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 55 removed outlier: 3.951A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.161A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 146 removed outlier: 7.428A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.461A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.004A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.929A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.792A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.936A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 723 removed outlier: 3.555A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 723 removed outlier: 3.555A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.510A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.563A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.921A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.882A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 135 through 145 removed outlier: 6.864A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.451A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.985A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.664A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.582A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.595A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.824A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 723 removed outlier: 3.789A pdb=" N VAL B1060 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 723 Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 3.545A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.431A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.959A 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: 3.773A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 68 through 70 removed outlier: 3.542A pdb=" N HIS C 69 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.575A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 142 through 146 removed outlier: 7.220A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.417A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.843A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.798A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.856A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.801A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.802A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.526A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C1060 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.559A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF4, first strand: chain 'H' and resid 9 through 13 removed outlier: 6.459A pdb=" N ILE H 39 " --> pdb=" O ASP H 55 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG H 64 " --> pdb=" O TYR H 57 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.620A pdb=" N ILE L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR L 55 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.698A pdb=" N THR L 117 " --> pdb=" O GLN L 106 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AF9, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AG1, first strand: chain 'M' and resid 9 through 13 removed outlier: 3.626A pdb=" N VAL M 13 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP M 38 " --> pdb=" O TYR M 107 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE M 39 " --> pdb=" O ASP M 55 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP M 55 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP M 41 " --> pdb=" O ILE M 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG M 64 " --> pdb=" O TYR M 57 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 9 through 13 removed outlier: 3.626A pdb=" N VAL M 13 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG M 106 " --> pdb=" O TYR M 117 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR M 117 " --> pdb=" O ARG M 106 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.746A pdb=" N ILE N 39 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR N 55 " --> pdb=" O ILE N 39 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AG6, first strand: chain 'P' and resid 3 through 5 removed outlier: 3.513A pdb=" N SER P 26 " --> pdb=" O GLN P 3 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN P 5 " --> pdb=" O LYS P 24 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS P 24 " --> pdb=" O GLN P 5 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.545A pdb=" N GLU P 11 " --> pdb=" O THR P 125 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY P 54 " --> pdb=" O TRP P 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS P 43 " --> pdb=" O TRP P 52 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP P 52 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG P 64 " --> pdb=" O TYR P 57 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 125 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE Q 39 " --> pdb=" O TYR Q 55 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR Q 55 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP Q 41 " --> pdb=" O LEU Q 53 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 125 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR Q 117 " --> pdb=" O GLN Q 106 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 30 through 31 1174 hydrogen bonds defined for protein. 3111 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: 15.35 Time building geometry restraints manager: 13.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9800 1.35 - 1.47: 7960 1.47 - 1.59: 13458 1.59 - 1.71: 0 1.71 - 1.83: 171 Bond restraints: 31389 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 ... (remaining 31384 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.04: 570 105.04 - 112.29: 15957 112.29 - 119.53: 9595 119.53 - 126.78: 16270 126.78 - 134.03: 355 Bond angle restraints: 42747 Sorted by residual: angle pdb=" CG ARG B 273 " pdb=" CD ARG B 273 " pdb=" NE ARG B 273 " ideal model delta sigma weight residual 112.00 101.83 10.17 2.20e+00 2.07e-01 2.14e+01 angle pdb=" N VAL M 111A" pdb=" CA VAL M 111A" pdb=" C VAL M 111A" ideal model delta sigma weight residual 112.98 109.16 3.82 1.25e+00 6.40e-01 9.36e+00 angle pdb=" CA LEU C 110 " pdb=" CB LEU C 110 " pdb=" CG LEU C 110 " ideal model delta sigma weight residual 116.30 126.78 -10.48 3.50e+00 8.16e-02 8.97e+00 angle pdb=" N VAL A 729 " pdb=" CA VAL A 729 " pdb=" C VAL A 729 " ideal model delta sigma weight residual 113.71 110.93 2.78 9.50e-01 1.11e+00 8.58e+00 angle pdb=" C TYR H 112 " pdb=" CA TYR H 112 " pdb=" CB TYR H 112 " ideal model delta sigma weight residual 110.42 116.03 -5.61 1.99e+00 2.53e-01 7.94e+00 ... (remaining 42742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.09: 18026 23.09 - 46.18: 912 46.18 - 69.27: 95 69.27 - 92.37: 43 92.37 - 115.46: 76 Dihedral angle restraints: 19152 sinusoidal: 7896 harmonic: 11256 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 7.45 85.55 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 104 " pdb=" CB CYS P 104 " ideal model delta sinusoidal sigma weight residual 93.00 36.09 56.91 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA TRP A 886 " pdb=" C TRP A 886 " pdb=" N THR A 887 " pdb=" CA THR A 887 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 19149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4703 0.099 - 0.198: 206 0.198 - 0.297: 9 0.297 - 0.395: 1 0.395 - 0.494: 1 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C1 NAG C1313 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1313 " pdb=" O5 NAG C1313 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" C1 NAG B1314 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1314 " pdb=" O5 NAG B1314 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C1 NAG B1313 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1313 " pdb=" O5 NAG B1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4917 not shown) Planarity restraints: 5523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 273 " 0.398 9.50e-02 1.11e+02 1.78e-01 2.01e+01 pdb=" NE ARG B 273 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 273 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 273 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 273 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 578 " -0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO B 579 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 579 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 579 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 84 " 0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO C 85 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.039 5.00e-02 4.00e+02 ... (remaining 5520 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1267 2.72 - 3.27: 30860 3.27 - 3.81: 49793 3.81 - 4.36: 58865 4.36 - 4.90: 99897 Nonbonded interactions: 240682 Sorted by model distance: nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.175 2.440 nonbonded pdb=" O GLU A 309 " pdb=" OH TYR A 313 " model vdw 2.188 2.440 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.188 2.520 nonbonded pdb=" O MET C 731 " pdb=" NE2 GLN C 774 " model vdw 2.197 2.520 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.200 2.440 ... (remaining 240677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } 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: 2.500 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: 11.510 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 84.780 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.220 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 0.053 31389 Z= 0.224 Angle : 0.590 10.480 42747 Z= 0.306 Chirality : 0.045 0.494 4920 Planarity : 0.005 0.178 5481 Dihedral : 15.469 115.458 11820 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.31 (0.13), residues: 3825 helix: 1.26 (0.20), residues: 680 sheet: 0.57 (0.17), residues: 910 loop : -0.23 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 886 HIS 0.005 0.001 HIS B 49 PHE 0.022 0.002 PHE C 86 TYR 0.020 0.001 TYR B 904 ARG 0.014 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 382 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.3774 time to fit residues: 246.1724 Evaluate side-chains 297 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 3.519 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 chunk 224 optimal weight: 7.9990 chunk 348 optimal weight: 50.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31389 Z= 0.305 Angle : 0.662 17.312 42747 Z= 0.332 Chirality : 0.048 0.349 4920 Planarity : 0.005 0.124 5481 Dihedral : 11.888 108.707 5064 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.94 % Allowed : 8.71 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.13), residues: 3825 helix: 1.06 (0.19), residues: 693 sheet: 0.59 (0.17), residues: 962 loop : -0.25 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 886 HIS 0.013 0.001 HIS B 49 PHE 0.025 0.002 PHE C 168 TYR 0.025 0.002 TYR B 170 ARG 0.010 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 328 time to evaluate : 3.440 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 22 residues processed: 347 average time/residue: 0.3820 time to fit residues: 229.7085 Evaluate side-chains 312 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 290 time to evaluate : 3.275 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2961 time to fit residues: 16.7596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 290 optimal weight: 0.6980 chunk 237 optimal weight: 0.0970 chunk 96 optimal weight: 0.8980 chunk 349 optimal weight: 9.9990 chunk 377 optimal weight: 0.3980 chunk 311 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 119 optimal weight: 0.9980 chunk 280 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 787 GLN A 965 GLN B 774 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 110 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 31389 Z= 0.160 Angle : 0.579 15.896 42747 Z= 0.283 Chirality : 0.045 0.323 4920 Planarity : 0.004 0.087 5481 Dihedral : 9.062 113.543 5064 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.73 % Allowed : 10.89 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.13), residues: 3825 helix: 1.35 (0.20), residues: 690 sheet: 0.51 (0.16), residues: 1010 loop : -0.21 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.014 0.001 HIS B 49 PHE 0.023 0.002 PHE C 55 TYR 0.015 0.001 TYR B 160 ARG 0.016 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 346 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 6 residues processed: 359 average time/residue: 0.3664 time to fit residues: 224.0961 Evaluate side-chains 303 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 297 time to evaluate : 2.633 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2787 time to fit residues: 7.3225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 30.0000 chunk 166 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 371 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 332 optimal weight: 50.0000 chunk 100 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 856 ASN A 895 GLN A 914 ASN B 777 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31389 Z= 0.282 Angle : 0.613 17.423 42747 Z= 0.305 Chirality : 0.046 0.330 4920 Planarity : 0.005 0.091 5481 Dihedral : 7.672 109.602 5064 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.72 % Allowed : 13.34 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.22 (0.13), residues: 3825 helix: 1.15 (0.19), residues: 682 sheet: 0.50 (0.17), residues: 981 loop : -0.31 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.009 0.001 HIS B 49 PHE 0.031 0.002 PHE C 275 TYR 0.027 0.001 TYR A 873 ARG 0.008 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 299 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 37 residues processed: 336 average time/residue: 0.3478 time to fit residues: 200.9918 Evaluate side-chains 313 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 276 time to evaluate : 2.672 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2713 time to fit residues: 23.5679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.0040 chunk 210 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 276 optimal weight: 1.9990 chunk 153 optimal weight: 40.0000 chunk 316 optimal weight: 20.0000 chunk 256 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.7980 chunk 333 optimal weight: 50.0000 chunk 93 optimal weight: 4.9990 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 196 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31389 Z= 0.311 Angle : 0.622 18.545 42747 Z= 0.313 Chirality : 0.046 0.315 4920 Planarity : 0.005 0.092 5481 Dihedral : 7.349 96.395 5064 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.66 % Allowed : 14.43 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.13 (0.13), residues: 3825 helix: 1.02 (0.19), residues: 680 sheet: 0.48 (0.17), residues: 964 loop : -0.34 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.004 0.001 HIS C1083 PHE 0.040 0.002 PHE C 275 TYR 0.022 0.001 TYR A 873 ARG 0.006 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 302 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 29 residues processed: 344 average time/residue: 0.2759 time to fit residues: 161.5659 Evaluate side-chains 306 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 277 time to evaluate : 2.056 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1912 time to fit residues: 13.2934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 0.0170 chunk 334 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 217 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 371 optimal weight: 10.0000 chunk 308 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 895 GLN A 901 GLN A 914 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31389 Z= 0.162 Angle : 0.559 16.758 42747 Z= 0.275 Chirality : 0.045 0.314 4920 Planarity : 0.004 0.076 5481 Dihedral : 6.801 89.192 5064 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.03 % Allowed : 15.25 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.25 (0.14), residues: 3825 helix: 1.27 (0.19), residues: 684 sheet: 0.45 (0.17), residues: 999 loop : -0.29 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.005 0.001 HIS C1048 PHE 0.038 0.001 PHE C 86 TYR 0.018 0.001 TYR B 160 ARG 0.005 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 309 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 328 average time/residue: 0.3882 time to fit residues: 215.9789 Evaluate side-chains 301 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 282 time to evaluate : 3.112 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2910 time to fit residues: 14.5892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 20.0000 chunk 41 optimal weight: 50.0000 chunk 211 optimal weight: 0.9990 chunk 271 optimal weight: 0.5980 chunk 210 optimal weight: 9.9990 chunk 312 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 370 optimal weight: 30.0000 chunk 231 optimal weight: 50.0000 chunk 225 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A1005 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2213 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: