Starting phenix.real_space_refine on Fri Jul 26 16:13:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc4_39922/07_2024/8zc4_39922.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc4_39922/07_2024/8zc4_39922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc4_39922/07_2024/8zc4_39922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc4_39922/07_2024/8zc4_39922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc4_39922/07_2024/8zc4_39922.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc4_39922/07_2024/8zc4_39922.cif" } resolution = 3.95 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= 0.034 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 144 5.16 5 C 21546 2.51 5 N 5560 2.21 5 O 6590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "G TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 86": "OD1" <-> "OD2" Residue "Q ASP 31": "OD1" <-> "OD2" Residue "Q TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.46s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 33840 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7790 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 55, 'TRANS': 938} Chain breaks: 10 Chain: "B" Number of atoms: 7790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7790 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 55, 'TRANS': 938} Chain breaks: 10 Chain: "C" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7778 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 55, 'TRANS': 937} Chain breaks: 10 Chain: "G" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "H" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "M" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "N" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "Q" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "R" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 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: "I" 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: "J" 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: "L" 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: "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: "T" 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: "U" 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: 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: "B" 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 17.02, per 1000 atoms: 0.50 Number of scatterers: 33840 At special positions: 0 Unit cell: (154.88, 211.2, 247.808, 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 144 16.00 O 6590 8.00 N 5560 7.00 C 21546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 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 538 " - pdb=" SG CYS A 590 " distance=2.04 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 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.04 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 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 145 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 145 " - pdb=" SG CYS M 204 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 145 " - pdb=" SG CYS N 204 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 103 " - pdb=" SG CYS Q 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 154 " - pdb=" SG CYS Q 210 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 108 " distance=2.03 Simple disulfide: pdb=" SG CYS R 154 " - pdb=" SG CYS R 210 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1098 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN B 122 " " NAG K 1 " - " ASN B 331 " " NAG L 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 11.71 Conformation dependent library (CDL) restraints added in 5.4 seconds 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8002 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 76 sheets defined 17.1% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.095A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.933A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.614A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.748A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.768A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.726A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 919 through 938 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.606A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.188A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (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 1146 removed outlier: 3.984A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.535A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.729A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 removed outlier: 3.874A pdb=" N ALA B 419 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP B 420 " --> pdb=" O ASN B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 420' Processing helix chain 'B' and resid 502 through 505 removed outlier: 3.589A pdb=" N HIS B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' 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 760 through 783 removed outlier: 3.839A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.559A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.762A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.871A 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 removed outlier: 3.519A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.428A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.687A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.768A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.876A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.709A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.615A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 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 removed outlier: 3.991A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.570A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.441A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 4.490A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 197 Processing helix chain 'M' and resid 132 through 138 removed outlier: 3.749A pdb=" N ALA M 138 " --> pdb=" O GLU M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 197 Processing helix chain 'N' and resid 132 through 138 removed outlier: 3.640A pdb=" N ALA N 138 " --> pdb=" O GLU N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 199 removed outlier: 3.553A pdb=" N HIS N 199 " --> pdb=" O GLN N 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.687A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 172 No H-bonds generated for 'chain 'Q' and resid 170 through 172' Processing helix chain 'R' and resid 106 through 111 removed outlier: 3.826A pdb=" N GLN R 109 " --> pdb=" O ASN R 106 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG R 110 " --> pdb=" O SER R 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP R 111 " --> pdb=" O CYS R 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 106 through 111' Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing helix chain 'R' and resid 199 through 203 removed outlier: 3.582A pdb=" N LEU R 203 " --> pdb=" O SER R 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.364A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.724A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.122A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.236A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.664A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.650A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.431A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB3, first strand: chain 'A' and resid 722 through 727 removed outlier: 3.602A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.880A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.245A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 578 " --> pdb=" O GLU C 583 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.728A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.759A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 314 through 319 removed outlier: 6.081A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.100A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 402 through 403 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 538 through 543 removed outlier: 4.014A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.158A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AC9, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.601A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.202A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.709A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS B1083 " --> pdb=" O LYS B1086 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.524A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.738A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.823A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.582A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 224 through 228 removed outlier: 5.234A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.666A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.053A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.364A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.154A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.716A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.665A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.594A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.728A pdb=" N THR G 108 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 18 through 23 removed outlier: 4.097A pdb=" N VAL G 18 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE G 76 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 20 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER G 66 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 45 through 49 removed outlier: 4.958A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP G 93 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY G 98 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.500A pdb=" N SER G 148 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR G 127 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL G 144 " --> pdb=" O PHE G 129 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA G 141 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS G 145 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP G 149 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR G 183 " --> pdb=" O ASP G 149 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.500A pdb=" N SER G 148 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR G 127 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL G 144 " --> pdb=" O PHE G 129 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA G 141 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS G 145 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP G 149 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR G 183 " --> pdb=" O ASP G 149 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA G 184 " --> pdb=" O SER G 176 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G 176 " --> pdb=" O ALA G 184 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 157 through 160 removed outlier: 4.199A pdb=" N VAL G 206 " --> pdb=" O VAL G 213 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL G 213 " --> pdb=" O VAL G 206 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.511A pdb=" N CYS H 22 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 46 through 50 removed outlier: 4.640A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 46 through 50 removed outlier: 4.640A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 150 through 159 removed outlier: 3.503A pdb=" N SER H 194 " --> pdb=" O CYS H 154 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP H 158 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 164 through 168 removed outlier: 3.750A pdb=" N THR H 165 " --> pdb=" O ASN H 213 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN H 213 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS H 210 " --> pdb=" O LYS H 223 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.534A pdb=" N ALA M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.534A pdb=" N ALA M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP M 93 " --> pdb=" O GLY M 98 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY M 98 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 17 through 23 Processing sheet with id=AG5, first strand: chain 'M' and resid 125 through 129 removed outlier: 3.802A pdb=" N VAL M 144 " --> pdb=" O PHE M 129 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP M 149 " --> pdb=" O TYR M 183 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR M 183 " --> pdb=" O ASP M 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA M 184 " --> pdb=" O SER M 176 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 157 through 160 removed outlier: 3.775A pdb=" N TYR M 202 " --> pdb=" O VAL M 217 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS M 204 " --> pdb=" O LYS M 215 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS M 215 " --> pdb=" O CYS M 204 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 9 through 11 removed outlier: 3.662A pdb=" N THR N 108 " --> pdb=" O ALA N 10 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 17 through 23 Processing sheet with id=AG9, first strand: chain 'N' and resid 46 through 49 removed outlier: 3.791A pdb=" N GLN N 38 " --> pdb=" O LYS N 46 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN N 39 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 125 through 129 removed outlier: 3.513A pdb=" N SER N 125 " --> pdb=" O SER N 148 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER N 148 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU N 146 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL N 144 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA N 141 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS N 145 " --> pdb=" O SER N 187 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER N 187 " --> pdb=" O CYS N 145 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 125 through 129 removed outlier: 3.513A pdb=" N SER N 125 " --> pdb=" O SER N 148 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER N 148 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU N 146 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL N 144 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE N 147 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR N 183 " --> pdb=" O ASP N 149 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 157 through 160 removed outlier: 3.897A pdb=" N ALA N 158 " --> pdb=" O GLN N 205 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN N 205 " --> pdb=" O ALA N 158 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS N 160 " --> pdb=" O SER N 203 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER N 203 " --> pdb=" O LYS N 160 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR N 202 " --> pdb=" O VAL N 217 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 17 through 18 Processing sheet with id=AH5, first strand: chain 'Q' and resid 45 through 47 removed outlier: 3.908A pdb=" N GLU Q 46 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG Q 38 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL Q 93 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 150 through 156 removed outlier: 3.538A pdb=" N CYS Q 154 " --> pdb=" O SER Q 194 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER Q 194 " --> pdb=" O CYS Q 154 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU Q 192 " --> pdb=" O VAL Q 156 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER Q 193 " --> pdb=" O PHE Q 180 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL Q 195 " --> pdb=" O HIS Q 178 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N HIS Q 178 " --> pdb=" O VAL Q 195 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 165 through 168 removed outlier: 4.244A pdb=" N THR Q 165 " --> pdb=" O ASN Q 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN Q 213 " --> pdb=" O THR Q 165 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 6 through 7 removed outlier: 3.701A pdb=" N SER R 21 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR R 69 " --> pdb=" O GLU R 82 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.628A pdb=" N LYS R 12 " --> pdb=" O THR R 124 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA R 121 " --> pdb=" O TYR R 94 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA R 92 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.628A pdb=" N LYS R 12 " --> pdb=" O THR R 124 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA R 121 " --> pdb=" O TYR R 94 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA R 92 " --> pdb=" O VAL R 123 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 134 through 136 removed outlier: 3.694A pdb=" N VAL R 198 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU R 152 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR R 190 " --> pdb=" O ASP R 158 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 134 through 136 removed outlier: 3.694A pdb=" N VAL R 198 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU R 152 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR R 190 " --> pdb=" O ASP R 158 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER R 191 " --> pdb=" O VAL R 183 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 165 through 168 removed outlier: 4.168A pdb=" N VAL R 212 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL R 221 " --> pdb=" O VAL R 212 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS R 214 " --> pdb=" O THR R 219 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR R 219 " --> pdb=" O HIS R 214 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 2859 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: 14.63 Time building geometry restraints manager: 12.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10658 1.34 - 1.47: 8784 1.47 - 1.60: 15019 1.60 - 1.72: 0 1.72 - 1.85: 180 Bond restraints: 34641 Sorted by residual: bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.41e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.99e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" CA GLN B 755 " pdb=" C GLN B 755 " ideal model delta sigma weight residual 1.522 1.491 0.030 1.43e-02 4.89e+03 4.52e+00 bond pdb=" CA ASP C1139 " pdb=" C ASP C1139 " ideal model delta sigma weight residual 1.526 1.502 0.024 1.25e-02 6.40e+03 3.55e+00 ... (remaining 34636 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.18: 1053 106.18 - 113.15: 18733 113.15 - 120.11: 11454 120.11 - 127.07: 15534 127.07 - 134.03: 392 Bond angle restraints: 47166 Sorted by residual: angle pdb=" N ASP C1118 " pdb=" CA ASP C1118 " pdb=" C ASP C1118 " ideal model delta sigma weight residual 113.02 103.36 9.66 1.49e+00 4.50e-01 4.21e+01 angle pdb=" N THR R 124 " pdb=" CA THR R 124 " pdb=" C THR R 124 " ideal model delta sigma weight residual 109.24 118.23 -8.99 1.51e+00 4.39e-01 3.54e+01 angle pdb=" N ASN C1119 " pdb=" CA ASN C1119 " pdb=" C ASN C1119 " ideal model delta sigma weight residual 113.89 105.55 8.34 1.58e+00 4.01e-01 2.79e+01 angle pdb=" N GLN B 755 " pdb=" CA GLN B 755 " pdb=" C GLN B 755 " ideal model delta sigma weight residual 112.87 107.51 5.36 1.20e+00 6.94e-01 2.00e+01 angle pdb=" C ASP C1139 " pdb=" N PRO C1140 " pdb=" CA PRO C1140 " ideal model delta sigma weight residual 120.31 115.95 4.36 9.80e-01 1.04e+00 1.98e+01 ... (remaining 47161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 19199 17.93 - 35.86: 1669 35.86 - 53.80: 299 53.80 - 71.73: 68 71.73 - 89.66: 38 Dihedral angle restraints: 21273 sinusoidal: 8841 harmonic: 12432 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -172.80 86.80 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -4.05 -81.95 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.87 -80.13 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 21270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4363 0.059 - 0.119: 1005 0.119 - 0.178: 99 0.178 - 0.238: 5 0.238 - 0.297: 5 Chirality restraints: 5477 Sorted by residual: chirality pdb=" CB ILE B 101 " pdb=" CA ILE B 101 " pdb=" CG1 ILE B 101 " pdb=" CG2 ILE B 101 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE A 410 " pdb=" CA ILE A 410 " pdb=" CG1 ILE A 410 " pdb=" CG2 ILE A 410 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 5474 not shown) Planarity restraints: 6037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 90 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C VAL C 90 " 0.071 2.00e-02 2.50e+03 pdb=" O VAL C 90 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR C 91 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.057 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO C 987 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.048 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 8.04e-02 1.03e+01 pdb=" N PRO B 987 " -0.139 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 6034 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4212 2.76 - 3.29: 30009 3.29 - 3.83: 54154 3.83 - 4.36: 57843 4.36 - 4.90: 105108 Nonbonded interactions: 251326 Sorted by model distance: nonbonded pdb=" OG1 THR A 912 " pdb=" OE1 GLN A1106 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.285 2.440 nonbonded pdb=" OH TYR M 35 " pdb=" O ARG Q 110 " model vdw 2.287 2.440 nonbonded pdb=" O PRO B 85 " pdb=" OH TYR B 269 " model vdw 2.288 2.440 ... (remaining 251321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1147 or resid 1301 through 1307)) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1147 or resid 1301 through 1307)) selection = (chain 'C' and (resid 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1147 or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'Q' selection = chain 'R' } 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=0.00 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: 1.120 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: 0.020 Extract box with map and model: 1.320 Check model and map are aligned: 0.220 Set scattering table: 0.320 Process input model: 84.070 Find NCS groups from input model: 3.790 Set up NCS constraints: 0.200 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34641 Z= 0.224 Angle : 0.705 10.004 47166 Z= 0.362 Chirality : 0.049 0.297 5477 Planarity : 0.006 0.085 6001 Dihedral : 13.867 89.660 13118 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.03 % Allowed : 0.48 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.57 (0.12), residues: 4193 helix: 0.22 (0.20), residues: 639 sheet: -0.11 (0.17), residues: 947 loop : -1.83 (0.11), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 47 HIS 0.005 0.001 HIS A1064 PHE 0.031 0.001 PHE Q 29 TYR 0.024 0.001 TYR C 489 ARG 0.005 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7199 (tp-100) cc_final: 0.6861 (pm20) REVERT: A 533 LEU cc_start: 0.7145 (mm) cc_final: 0.6912 (mm) REVERT: A 1029 MET cc_start: 0.9319 (tpp) cc_final: 0.9081 (tpp) REVERT: A 1141 LEU cc_start: 0.8324 (mm) cc_final: 0.8085 (mm) REVERT: B 269 TYR cc_start: 0.8052 (m-80) cc_final: 0.7777 (m-80) REVERT: B 1017 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7688 (tm-30) REVERT: C 135 PHE cc_start: 0.5785 (m-80) cc_final: 0.5518 (m-80) REVERT: C 697 MET cc_start: 0.8278 (tpp) cc_final: 0.7900 (mmt) REVERT: C 823 PHE cc_start: 0.7896 (t80) cc_final: 0.7631 (t80) REVERT: C 1029 MET cc_start: 0.9124 (tpp) cc_final: 0.8835 (tpp) outliers start: 1 outliers final: 1 residues processed: 272 average time/residue: 0.4191 time to fit residues: 192.9943 Evaluate side-chains 183 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 50.0000 chunk 322 optimal weight: 30.0000 chunk 179 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 333 optimal weight: 30.0000 chunk 129 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 386 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 493 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 271 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 755 GLN B 926 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 505 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN R 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 34641 Z= 0.581 Angle : 0.766 11.899 47166 Z= 0.394 Chirality : 0.050 0.297 5477 Planarity : 0.006 0.081 6001 Dihedral : 6.085 48.290 5573 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.16 % Allowed : 9.52 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.12), residues: 4193 helix: 0.05 (0.19), residues: 667 sheet: -0.31 (0.17), residues: 988 loop : -1.83 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 47 HIS 0.011 0.001 HIS Q 35 PHE 0.032 0.003 PHE C 92 TYR 0.024 0.002 TYR C1067 ARG 0.009 0.001 ARG Q 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 195 time to evaluate : 3.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7420 (tp-100) cc_final: 0.6978 (pm20) REVERT: A 227 VAL cc_start: 0.8294 (m) cc_final: 0.8052 (t) REVERT: A 578 ASP cc_start: 0.7612 (p0) cc_final: 0.7385 (p0) REVERT: B 53 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7183 (m-30) REVERT: C 135 PHE cc_start: 0.6275 (m-80) cc_final: 0.6004 (m-80) REVERT: C 394 ASN cc_start: 0.7114 (m110) cc_final: 0.6866 (m-40) REVERT: C 508 TYR cc_start: 0.8218 (m-80) cc_final: 0.7625 (m-80) REVERT: C 523 THR cc_start: 0.8576 (p) cc_final: 0.8242 (t) REVERT: C 708 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8210 (p) REVERT: C 823 PHE cc_start: 0.8219 (t80) cc_final: 0.7962 (t80) REVERT: Q 32 TYR cc_start: 0.8563 (m-80) cc_final: 0.8266 (m-10) outliers start: 43 outliers final: 32 residues processed: 229 average time/residue: 0.4099 time to fit residues: 161.4665 Evaluate side-chains 196 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain R residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 321 optimal weight: 6.9990 chunk 263 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 387 optimal weight: 0.0370 chunk 418 optimal weight: 50.0000 chunk 345 optimal weight: 0.1980 chunk 384 optimal weight: 0.0980 chunk 132 optimal weight: 2.9990 chunk 310 optimal weight: 50.0000 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN B 196 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C1036 GLN H 35 HIS H 109 GLN R 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 34641 Z= 0.140 Angle : 0.528 12.144 47166 Z= 0.267 Chirality : 0.043 0.240 5477 Planarity : 0.004 0.079 6001 Dihedral : 5.219 48.163 5573 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.81 % Allowed : 12.00 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.20 (0.13), residues: 4193 helix: 1.14 (0.21), residues: 648 sheet: -0.16 (0.17), residues: 972 loop : -1.65 (0.12), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP Q 113 HIS 0.005 0.001 HIS Q 35 PHE 0.018 0.001 PHE C 55 TYR 0.015 0.001 TYR C1067 ARG 0.003 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 228 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6887 (p0) REVERT: C 135 PHE cc_start: 0.6058 (m-80) cc_final: 0.5813 (m-80) REVERT: C 508 TYR cc_start: 0.8088 (m-80) cc_final: 0.7507 (m-80) REVERT: C 708 SER cc_start: 0.8179 (t) cc_final: 0.7966 (p) REVERT: C 823 PHE cc_start: 0.8052 (t80) cc_final: 0.7766 (t80) REVERT: C 878 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7829 (mm) REVERT: C 904 TYR cc_start: 0.8059 (m-80) cc_final: 0.7668 (m-10) REVERT: M 88 TYR cc_start: 0.5225 (m-10) cc_final: 0.4890 (m-10) REVERT: Q 31 ASP cc_start: 0.7995 (p0) cc_final: 0.7629 (p0) REVERT: Q 32 TYR cc_start: 0.8282 (m-80) cc_final: 0.8079 (m-80) REVERT: R 87 ARG cc_start: 0.5470 (mmp80) cc_final: 0.5261 (mmp-170) outliers start: 30 outliers final: 19 residues processed: 220 average time/residue: 0.4579 time to fit residues: 172.3535 Evaluate side-chains 195 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain H residue 124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 9.9990 chunk 291 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 388 optimal weight: 10.0000 chunk 411 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 368 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 907 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 34641 Z= 0.384 Angle : 0.638 12.292 47166 Z= 0.323 Chirality : 0.046 0.255 5477 Planarity : 0.005 0.067 6001 Dihedral : 5.331 45.184 5572 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.39 % Allowed : 13.37 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.40 (0.13), residues: 4193 helix: 0.70 (0.20), residues: 662 sheet: -0.37 (0.16), residues: 1012 loop : -1.70 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Q 113 HIS 0.016 0.001 HIS G 99 PHE 0.027 0.002 PHE C 92 TYR 0.020 0.002 TYR C 904 ARG 0.006 0.000 ARG Q 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 184 time to evaluate : 4.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7370 (tp-100) cc_final: 0.6932 (pm20) REVERT: A 578 ASP cc_start: 0.7766 (p0) cc_final: 0.7491 (p0) REVERT: A 1031 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: B 759 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6757 (t80) REVERT: C 135 PHE cc_start: 0.6008 (m-80) cc_final: 0.5716 (m-80) REVERT: C 275 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8484 (m-10) REVERT: C 508 TYR cc_start: 0.8208 (m-80) cc_final: 0.7589 (m-80) REVERT: C 523 THR cc_start: 0.8776 (p) cc_final: 0.8283 (t) REVERT: C 697 MET cc_start: 0.8607 (tpp) cc_final: 0.8405 (tpt) REVERT: C 708 SER cc_start: 0.8459 (t) cc_final: 0.8256 (p) REVERT: C 767 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8137 (mt) REVERT: C 823 PHE cc_start: 0.8209 (t80) cc_final: 0.7948 (t80) REVERT: C 878 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7916 (mm) REVERT: Q 31 ASP cc_start: 0.7864 (p0) cc_final: 0.7291 (p0) REVERT: Q 32 TYR cc_start: 0.8596 (m-80) cc_final: 0.8143 (m-80) outliers start: 89 outliers final: 62 residues processed: 264 average time/residue: 0.4180 time to fit residues: 189.1353 Evaluate side-chains 241 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 174 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 ASP Chi-restraints excluded: chain R residue 70 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 3.9990 chunk 233 optimal weight: 0.0970 chunk 5 optimal weight: 5.9990 chunk 306 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 351 optimal weight: 8.9990 chunk 284 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 210 optimal weight: 0.9980 chunk 369 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34641 Z= 0.318 Angle : 0.591 12.882 47166 Z= 0.299 Chirality : 0.045 0.250 5477 Planarity : 0.004 0.063 6001 Dihedral : 5.246 44.140 5572 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.47 % Allowed : 14.82 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.36 (0.13), residues: 4193 helix: 0.95 (0.21), residues: 646 sheet: -0.42 (0.16), residues: 1027 loop : -1.69 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP Q 113 HIS 0.005 0.001 HIS G 99 PHE 0.023 0.002 PHE C 92 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG R 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 188 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 ASP cc_start: 0.7819 (p0) cc_final: 0.7577 (p0) REVERT: B 759 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6719 (t80) REVERT: C 135 PHE cc_start: 0.5916 (m-80) cc_final: 0.5694 (m-80) REVERT: C 275 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8347 (m-10) REVERT: C 508 TYR cc_start: 0.8171 (m-80) cc_final: 0.7616 (m-80) REVERT: C 523 THR cc_start: 0.8774 (p) cc_final: 0.8208 (t) REVERT: C 823 PHE cc_start: 0.8182 (t80) cc_final: 0.7903 (t80) REVERT: C 878 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7964 (mm) REVERT: C 1029 MET cc_start: 0.9145 (tpp) cc_final: 0.8878 (tpp) REVERT: M 88 TYR cc_start: 0.4716 (m-10) cc_final: 0.4092 (m-10) REVERT: Q 31 ASP cc_start: 0.7870 (p0) cc_final: 0.7264 (p0) REVERT: Q 32 TYR cc_start: 0.8607 (m-80) cc_final: 0.8123 (m-10) outliers start: 92 outliers final: 71 residues processed: 272 average time/residue: 0.3975 time to fit residues: 186.1127 Evaluate side-chains 247 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 173 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 117 TRP Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 ASP Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 131 LYS Chi-restraints excluded: chain R residue 221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 10.0000 chunk 370 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 412 optimal weight: 20.0000 chunk 342 optimal weight: 7.9990 chunk 190 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 216 optimal weight: 0.6980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 34641 Z= 0.403 Angle : 0.644 12.847 47166 Z= 0.326 Chirality : 0.046 0.259 5477 Planarity : 0.005 0.061 6001 Dihedral : 5.407 47.671 5572 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.55 % Allowed : 15.84 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.54 (0.13), residues: 4193 helix: 0.59 (0.20), residues: 661 sheet: -0.53 (0.16), residues: 1031 loop : -1.76 (0.12), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP Q 113 HIS 0.005 0.001 HIS M 99 PHE 0.026 0.002 PHE C 92 TYR 0.018 0.002 TYR C1067 ARG 0.006 0.000 ARG R 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 179 time to evaluate : 4.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 ASP cc_start: 0.7970 (p0) cc_final: 0.7746 (p0) REVERT: B 228 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6763 (p0) REVERT: B 759 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6774 (t80) REVERT: C 135 PHE cc_start: 0.6036 (m-80) cc_final: 0.5700 (m-80) REVERT: C 275 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8337 (m-10) REVERT: C 508 TYR cc_start: 0.8189 (m-80) cc_final: 0.7602 (m-80) REVERT: C 697 MET cc_start: 0.8492 (tpp) cc_final: 0.8145 (tpt) REVERT: C 823 PHE cc_start: 0.8161 (t80) cc_final: 0.7916 (t80) REVERT: C 878 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7948 (mm) REVERT: C 1029 MET cc_start: 0.9143 (tpp) cc_final: 0.8917 (tpp) REVERT: G 99 HIS cc_start: 0.2693 (OUTLIER) cc_final: 0.2136 (m-70) REVERT: M 62 ARG cc_start: 0.5656 (tpt90) cc_final: 0.5117 (tpt90) REVERT: M 88 TYR cc_start: 0.5011 (m-10) cc_final: 0.4746 (m-10) REVERT: Q 31 ASP cc_start: 0.7930 (p0) cc_final: 0.7537 (p0) REVERT: Q 32 TYR cc_start: 0.8599 (m-80) cc_final: 0.8171 (m-10) REVERT: Q 64 PHE cc_start: 0.6341 (m-10) cc_final: 0.6084 (m-80) outliers start: 132 outliers final: 104 residues processed: 296 average time/residue: 0.4131 time to fit residues: 211.4616 Evaluate side-chains 281 residues out of total 3718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 172 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 117 TRP Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 ASP Chi-restraints excluded: chain R residue 56 ASP Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.9677 > 50: distance: 10 - 193: 6.570 distance: 20 - 182: 5.830 distance: 23 - 179: 5.967 distance: 127 - 131: 7.340 distance: 131 - 132: 15.181 distance: 131 - 137: 23.477 distance: 132 - 133: 11.053 distance: 132 - 135: 19.007 distance: 133 - 134: 41.864 distance: 133 - 138: 13.535 distance: 135 - 136: 18.426 distance: 136 - 137: 11.868 distance: 138 - 139: 13.405 distance: 139 - 140: 14.475 distance: 139 - 142: 26.683 distance: 140 - 141: 18.574 distance: 140 - 147: 11.917 distance: 142 - 143: 7.750 distance: 143 - 144: 21.064 distance: 144 - 145: 21.308 distance: 144 - 146: 20.814 distance: 147 - 148: 11.597 distance: 148 - 149: 4.571 distance: 148 - 151: 4.339 distance: 149 - 150: 13.754 distance: 149 - 153: 11.030 distance: 151 - 152: 16.856 distance: 153 - 154: 9.932 distance: 154 - 155: 6.436 distance: 154 - 157: 8.333 distance: 155 - 156: 16.118 distance: 155 - 158: 5.471 distance: 158 - 159: 11.183 distance: 158 - 164: 8.349 distance: 159 - 160: 4.116 distance: 159 - 162: 5.467 distance: 160 - 161: 15.829 distance: 160 - 165: 12.100 distance: 162 - 163: 12.767 distance: 163 - 164: 6.218 distance: 165 - 166: 6.999 distance: 166 - 167: 3.914 distance: 166 - 169: 9.285 distance: 167 - 168: 12.825 distance: 167 - 175: 5.824 distance: 169 - 170: 8.151 distance: 170 - 171: 14.861 distance: 170 - 172: 11.363 distance: 171 - 173: 3.472 distance: 172 - 174: 4.889 distance: 173 - 174: 5.315 distance: 175 - 176: 12.984 distance: 176 - 177: 10.914 distance: 177 - 178: 10.106 distance: 177 - 179: 5.300 distance: 179 - 180: 5.714 distance: 180 - 181: 11.495 distance: 180 - 183: 6.110 distance: 181 - 182: 14.626 distance: 181 - 186: 14.125 distance: 183 - 184: 5.875 distance: 183 - 185: 7.898 distance: 186 - 187: 7.914 distance: 187 - 188: 14.698 distance: 187 - 190: 6.338 distance: 188 - 189: 17.324 distance: 188 - 193: 15.363 distance: 190 - 191: 14.744 distance: 190 - 192: 9.102 distance: 193 - 194: 3.144 distance: 194 - 195: 6.921 distance: 194 - 197: 11.545 distance: 195 - 196: 5.172 distance: 195 - 204: 3.949 distance: 197 - 198: 3.449 distance: 198 - 199: 7.136 distance: 198 - 200: 10.181 distance: 199 - 201: 7.875 distance: 200 - 202: 9.326 distance: 201 - 203: 6.381 distance: 202 - 203: 10.104