Starting phenix.real_space_refine on Thu Mar 21 18:28:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a94_15269/03_2024/8a94_15269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a94_15269/03_2024/8a94_15269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a94_15269/03_2024/8a94_15269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a94_15269/03_2024/8a94_15269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a94_15269/03_2024/8a94_15269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a94_15269/03_2024/8a94_15269.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.086 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 135 5.16 5 C 19598 2.51 5 N 5069 2.21 5 O 6060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30862 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8292 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1008} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8290 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1008} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8244 Classifications: {'peptide': 1056} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "O" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "T" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 16.09, per 1000 atoms: 0.52 Number of scatterers: 30862 At special positions: 0 Unit cell: (159.58, 161.6, 229.27, 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 135 16.00 O 6060 8.00 N 5069 7.00 C 19598 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 89 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 149 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 801 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 603 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 149 " " NAG C1311 " - " ASN C 331 " " NAG C1312 " - " ASN C 343 " " NAG C1313 " - " ASN C 61 " " NAG C1314 " - " ASN C 165 " " NAG C1315 " - " ASN C 234 " " NAG C1316 " - " ASN C 801 " " NAG G 1 " - " ASN A 61 " " NAG H 1 " - " ASN A 17 " " NAG J 1 " - " ASN A 234 " " NAG L 1 " - " ASN B 122 " " NAG M 1 " - " ASN C 17 " Time building additional restraints: 12.39 Conformation dependent library (CDL) restraints added in 5.6 seconds 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7182 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 63 sheets defined 20.7% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 372 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 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.684A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.582A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.879A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 912 through 940 removed outlier: 4.351A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.754A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.031A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 removed outlier: 4.307A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.649A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.703A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.075A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.766A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.511A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.972A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.928A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.538A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.994A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.596A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.940A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'R' and resid 27 through 32 removed outlier: 4.097A pdb=" N THR R 31 " --> pdb=" O GLY R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 removed outlier: 4.184A pdb=" N THR R 91 " --> pdb=" O TYR R 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 32 removed outlier: 4.037A pdb=" N THR T 31 " --> pdb=" O GLY T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 91 removed outlier: 4.166A pdb=" N THR T 91 " --> pdb=" O TYR T 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 33 removed outlier: 4.029A pdb=" N SER Q 32 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR Q 33 " --> pdb=" O SER Q 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 29 through 33' Processing helix chain 'K' and resid 27 through 32 removed outlier: 4.208A pdb=" N THR K 31 " --> pdb=" O GLY K 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 32 removed outlier: 3.681A pdb=" N SER E 32 " --> pdb=" O VAL E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.813A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.576A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.969A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.882A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.634A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.616A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.665A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.524A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.118A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.885A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.569A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.569A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.362A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.147A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.125A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.773A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 126 through 128 removed outlier: 5.892A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.638A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.439A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.607A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 551 through 554 removed outlier: 4.944A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.102A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.763A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.572A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.375A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.372A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.219A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 13.140A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.500A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.664A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.848A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.462A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.613A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.264A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.347A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.347A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.535A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'R' and resid 9 through 11 removed outlier: 3.861A pdb=" N THR R 120 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL R 37 " --> pdb=" O TYR R 95 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE R 34 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 18 through 19 removed outlier: 3.604A pdb=" N VAL R 18 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 18 through 19 removed outlier: 3.604A pdb=" N VAL R 18 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 34 through 39 removed outlier: 6.507A pdb=" N LEU O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR O 50 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 9 through 11 removed outlier: 3.875A pdb=" N THR T 120 " --> pdb=" O GLU T 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL T 37 " --> pdb=" O TYR T 95 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE T 34 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG T 50 " --> pdb=" O ILE T 34 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP T 36 " --> pdb=" O MET T 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 9 through 11 removed outlier: 3.875A pdb=" N THR T 120 " --> pdb=" O GLU T 10 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR T 112 " --> pdb=" O ARG T 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 18 through 19 removed outlier: 3.617A pdb=" N VAL T 18 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 18 through 19 removed outlier: 3.617A pdb=" N VAL T 18 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 4 through 5 Processing sheet with id=AG3, first strand: chain 'Q' and resid 54 through 55 removed outlier: 6.502A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR Q 50 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.592A pdb=" N THR K 120 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.592A pdb=" N THR K 120 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR K 112 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 18 through 23 removed outlier: 3.674A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AG8, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.642A pdb=" N SER E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 63 through 65 1161 hydrogen bonds defined for protein. 3177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.23 Time building geometry restraints manager: 13.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8424 1.33 - 1.46: 9044 1.46 - 1.59: 13915 1.59 - 1.72: 2 1.72 - 1.85: 173 Bond restraints: 31558 Sorted by residual: bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.335 1.404 -0.068 1.30e-02 5.92e+03 2.77e+01 bond pdb=" CB PRO B 230 " pdb=" CG PRO B 230 " ideal model delta sigma weight residual 1.492 1.274 0.218 5.00e-02 4.00e+02 1.91e+01 bond pdb=" N GLY A 431 " pdb=" CA GLY A 431 " ideal model delta sigma weight residual 1.445 1.476 -0.031 8.30e-03 1.45e+04 1.40e+01 bond pdb=" N VAL B 16 " pdb=" CA VAL B 16 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.11e-02 8.12e+03 1.40e+01 bond pdb=" C LYS B 462 " pdb=" N PRO B 463 " ideal model delta sigma weight residual 1.330 1.373 -0.042 1.19e-02 7.06e+03 1.27e+01 ... (remaining 31553 not shown) Histogram of bond angle deviations from ideal: 90.20 - 99.14: 8 99.14 - 108.08: 1670 108.08 - 117.02: 21032 117.02 - 125.96: 19764 125.96 - 134.90: 458 Bond angle restraints: 42932 Sorted by residual: angle pdb=" N ALA A 522 " pdb=" CA ALA A 522 " pdb=" C ALA A 522 " ideal model delta sigma weight residual 111.24 121.13 -9.89 1.38e+00 5.25e-01 5.14e+01 angle pdb=" N PRO A 899 " pdb=" CA PRO A 899 " pdb=" CB PRO A 899 " ideal model delta sigma weight residual 103.25 110.70 -7.45 1.05e+00 9.07e-01 5.03e+01 angle pdb=" CG1 ILE A 402 " pdb=" CB ILE A 402 " pdb=" CG2 ILE A 402 " ideal model delta sigma weight residual 110.70 90.20 20.50 3.00e+00 1.11e-01 4.67e+01 angle pdb=" N PRO B 899 " pdb=" CA PRO B 899 " pdb=" CB PRO B 899 " ideal model delta sigma weight residual 103.51 109.87 -6.36 9.60e-01 1.09e+00 4.39e+01 angle pdb=" C GLN E 101 " pdb=" N GLY E 102 " pdb=" CA GLY E 102 " ideal model delta sigma weight residual 121.41 108.54 12.87 1.96e+00 2.60e-01 4.31e+01 ... (remaining 42927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 18052 21.33 - 42.65: 1134 42.65 - 63.98: 197 63.98 - 85.31: 54 85.31 - 106.64: 27 Dihedral angle restraints: 19464 sinusoidal: 8254 harmonic: 11210 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -174.44 88.44 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -148.95 62.95 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -27.79 -58.21 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 19461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 4933 0.225 - 0.449: 46 0.449 - 0.674: 3 0.674 - 0.898: 0 0.898 - 1.123: 1 Chirality restraints: 4983 Sorted by residual: chirality pdb=" CB THR A 523 " pdb=" CA THR A 523 " pdb=" OG1 THR A 523 " pdb=" CG2 THR A 523 " both_signs ideal model delta sigma weight residual False 2.55 1.43 1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.45e+00 ... (remaining 4980 not shown) Planarity restraints: 5533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " -0.350 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG C1301 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " 0.528 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG C1303 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.505 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1302 " 0.294 2.00e-02 2.50e+03 2.52e-01 7.91e+02 pdb=" C7 NAG C1302 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C1302 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG C1302 " -0.439 2.00e-02 2.50e+03 pdb=" O7 NAG C1302 " 0.042 2.00e-02 2.50e+03 ... (remaining 5530 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 332 2.62 - 3.19: 25363 3.19 - 3.76: 48515 3.76 - 4.33: 67018 4.33 - 4.90: 110489 Nonbonded interactions: 251717 Sorted by model distance: nonbonded pdb=" O PRO C 600 " pdb=" CG2 THR C 604 " model vdw 2.046 3.460 nonbonded pdb=" O TYR E 50 " pdb=" OG SER E 54 " model vdw 2.178 2.440 nonbonded pdb=" OG1 THR T 120 " pdb=" O SER T 122 " model vdw 2.230 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.262 2.440 ... (remaining 251712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 577 or resid 584 through 1146 o \ r resid 1301 through 1313)) selection = (chain 'B' and (resid 14 through 577 or resid 584 through 1146 or resid 1301 thr \ ough 1313)) selection = (chain 'C' and (resid 14 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 1146 or resid 1301 through 1313 \ )) } ncs_group { reference = chain 'E' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 28.000 Check model and map are aligned: 0.460 Set scattering table: 0.300 Process input model: 86.520 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.310 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 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 : 0.007 0.218 31558 Z= 0.478 Angle : 1.104 20.503 42932 Z= 0.610 Chirality : 0.073 1.123 4983 Planarity : 0.010 0.299 5487 Dihedral : 14.510 106.635 12156 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 0.66 % Allowed : 0.96 % Favored : 98.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 3814 helix: 2.09 (0.20), residues: 678 sheet: -0.30 (0.17), residues: 944 loop : -1.30 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 886 HIS 0.012 0.002 HIS C1048 PHE 0.068 0.004 PHE B 377 TYR 0.058 0.003 TYR B 508 ARG 0.021 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 574 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 919 ASN cc_start: 0.5895 (m-40) cc_final: 0.5563 (m110) REVERT: C 177 MET cc_start: 0.1518 (ttt) cc_final: 0.0923 (mpt) REVERT: C 384 PRO cc_start: 0.5205 (Cg_endo) cc_final: 0.4681 (Cg_exo) REVERT: T 82 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8297 (tm-30) REVERT: T 110 LEU cc_start: 0.7766 (mt) cc_final: 0.7486 (mt) outliers start: 22 outliers final: 4 residues processed: 594 average time/residue: 1.1768 time to fit residues: 846.6585 Evaluate side-chains 298 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 294 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain K residue 7 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 20.0000 chunk 290 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 300 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 347 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 774 GLN A 901 GLN A 914 ASN A 954 GLN A 969 ASN B 49 HIS B 81 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 954 GLN B 957 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C1002 GLN C1106 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 31558 Z= 0.309 Angle : 0.768 15.244 42932 Z= 0.387 Chirality : 0.054 0.480 4983 Planarity : 0.005 0.068 5487 Dihedral : 9.055 77.528 5376 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 2.77 % Allowed : 13.11 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 3814 helix: 1.89 (0.20), residues: 664 sheet: -0.24 (0.17), residues: 927 loop : -1.33 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 886 HIS 0.007 0.001 HIS C1048 PHE 0.039 0.003 PHE B 898 TYR 0.029 0.002 TYR C1067 ARG 0.010 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 337 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ASN cc_start: -0.1733 (OUTLIER) cc_final: -0.2050 (m-40) REVERT: C 177 MET cc_start: 0.1930 (ttt) cc_final: 0.0996 (mpt) REVERT: C 1077 THR cc_start: 0.7596 (p) cc_final: 0.7248 (t) REVERT: R 48 MET cc_start: 0.8649 (mtp) cc_final: 0.8415 (mtm) REVERT: O 36 TRP cc_start: 0.7432 (m100) cc_final: 0.7222 (m100) REVERT: O 74 LEU cc_start: 0.5639 (tm) cc_final: 0.5423 (tt) REVERT: T 12 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.7736 (ttmt) REVERT: T 23 LYS cc_start: 0.8827 (tptp) cc_final: 0.8507 (tppt) REVERT: T 70 PHE cc_start: 0.7259 (m-10) cc_final: 0.6406 (m-80) REVERT: Q 21 LEU cc_start: 0.7333 (mt) cc_final: 0.7100 (mm) REVERT: Q 80 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8612 (mm-30) REVERT: K 54 MET cc_start: 0.3508 (OUTLIER) cc_final: 0.3096 (pmm) outliers start: 92 outliers final: 34 residues processed: 404 average time/residue: 1.0755 time to fit residues: 536.4232 Evaluate side-chains 293 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 256 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 193 optimal weight: 0.8980 chunk 107 optimal weight: 0.0980 chunk 289 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 348 optimal weight: 8.9990 chunk 376 optimal weight: 50.0000 chunk 310 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 279 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 919 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 49 HIS B 81 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN B 957 GLN B1011 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C1002 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31558 Z= 0.262 Angle : 0.692 11.942 42932 Z= 0.355 Chirality : 0.050 0.586 4983 Planarity : 0.005 0.062 5487 Dihedral : 7.858 70.458 5370 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 3.79 % Allowed : 15.18 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 3814 helix: 1.93 (0.20), residues: 647 sheet: -0.42 (0.16), residues: 931 loop : -1.34 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 104 HIS 0.004 0.001 HIS C1088 PHE 0.032 0.002 PHE B 135 TYR 0.021 0.002 TYR C1067 ARG 0.012 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 303 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLN cc_start: -0.0889 (OUTLIER) cc_final: -0.1431 (pp30) REVERT: B 177 MET cc_start: 0.2257 (ttt) cc_final: 0.0559 (mmt) REVERT: B 577 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.5957 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6464 (tt0) REVERT: C 177 MET cc_start: 0.1751 (ttt) cc_final: 0.0318 (mpt) REVERT: T 70 PHE cc_start: 0.7397 (m-10) cc_final: 0.6426 (m-80) REVERT: T 118 LEU cc_start: 0.8626 (tm) cc_final: 0.8083 (mm) REVERT: Q 88 TYR cc_start: 0.7336 (m-80) cc_final: 0.6778 (m-80) REVERT: K 48 MET cc_start: 0.1622 (ptp) cc_final: -0.1086 (ptt) REVERT: K 102 TYR cc_start: 0.2168 (m-80) cc_final: 0.1443 (m-80) outliers start: 126 outliers final: 52 residues processed: 395 average time/residue: 1.0556 time to fit residues: 516.7505 Evaluate side-chains 303 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 248 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 88 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 344 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 166 optimal weight: 0.3980 chunk 233 optimal weight: 3.9990 chunk 349 optimal weight: 9.9990 chunk 370 optimal weight: 40.0000 chunk 182 optimal weight: 0.7980 chunk 331 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 919 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 542 ASN B 779 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1002 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 31558 Z= 0.311 Angle : 0.708 10.093 42932 Z= 0.362 Chirality : 0.051 0.472 4983 Planarity : 0.005 0.088 5487 Dihedral : 7.400 64.178 5370 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 4.45 % Allowed : 16.96 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3814 helix: 1.69 (0.19), residues: 663 sheet: -0.54 (0.16), residues: 999 loop : -1.42 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 104 HIS 0.004 0.001 HIS B1058 PHE 0.028 0.002 PHE B 898 TYR 0.027 0.002 TYR K 101 ARG 0.007 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 269 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ILE cc_start: 0.1397 (OUTLIER) cc_final: 0.0968 (mm) REVERT: B 314 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: B 577 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.6210 (ptp-170) REVERT: B 1113 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6624 (mt0) REVERT: C 100 ILE cc_start: 0.6219 (mp) cc_final: 0.5949 (mp) REVERT: C 177 MET cc_start: 0.1680 (ttt) cc_final: 0.0425 (mpt) REVERT: C 365 TYR cc_start: 0.6408 (OUTLIER) cc_final: 0.6070 (m-80) REVERT: C 780 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6276 (pp20) REVERT: R 48 MET cc_start: 0.7542 (ptp) cc_final: 0.7276 (mpp) REVERT: R 54 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5967 (mpp) REVERT: T 81 MET cc_start: 0.8059 (mtp) cc_final: 0.7619 (mtp) REVERT: T 82 GLU cc_start: 0.7264 (tp30) cc_final: 0.6933 (tp30) REVERT: T 118 LEU cc_start: 0.8375 (tm) cc_final: 0.7606 (mm) REVERT: Q 76 ILE cc_start: 0.7778 (tp) cc_final: 0.7514 (pp) REVERT: Q 88 TYR cc_start: 0.7486 (m-80) cc_final: 0.7210 (m-80) REVERT: K 60 TYR cc_start: 0.4398 (OUTLIER) cc_final: 0.4099 (t80) REVERT: K 102 TYR cc_start: 0.2033 (m-80) cc_final: 0.0988 (m-80) outliers start: 148 outliers final: 68 residues processed: 376 average time/residue: 1.0561 time to fit residues: 495.7197 Evaluate side-chains 317 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 241 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 62 ARG Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 88 TYR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 88 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 308 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 315 optimal weight: 0.8980 chunk 255 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 332 optimal weight: 40.0000 chunk 93 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 920 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN R 43 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31558 Z= 0.335 Angle : 0.721 13.743 42932 Z= 0.372 Chirality : 0.051 0.445 4983 Planarity : 0.005 0.079 5487 Dihedral : 7.069 59.797 5370 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 4.60 % Allowed : 17.86 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 3814 helix: 1.57 (0.19), residues: 657 sheet: -0.65 (0.16), residues: 987 loop : -1.49 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 104 HIS 0.004 0.001 HIS B1058 PHE 0.052 0.002 PHE T 29 TYR 0.025 0.002 TYR K 94 ARG 0.007 0.001 ARG T 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 279 time to evaluate : 4.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 558 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6521 (mmmm) REVERT: B 762 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6444 (tm-30) REVERT: C 177 MET cc_start: 0.1668 (ttt) cc_final: 0.0804 (mpt) REVERT: C 780 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6264 (pp20) REVERT: C 1031 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: R 48 MET cc_start: 0.7727 (ptp) cc_final: 0.7373 (mpp) REVERT: R 54 MET cc_start: 0.6584 (mpp) cc_final: 0.6047 (mpp) REVERT: R 81 MET cc_start: 0.0111 (mmm) cc_final: -0.0159 (mmm) REVERT: T 70 PHE cc_start: 0.7261 (m-10) cc_final: 0.6854 (m-80) REVERT: T 90 ASP cc_start: 0.8125 (m-30) cc_final: 0.7443 (m-30) REVERT: T 118 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7823 (mm) REVERT: Q 88 TYR cc_start: 0.7557 (m-80) cc_final: 0.7345 (m-80) REVERT: K 60 TYR cc_start: 0.3993 (OUTLIER) cc_final: 0.3529 (t80) REVERT: K 102 TYR cc_start: 0.1559 (m-80) cc_final: 0.0676 (m-80) outliers start: 153 outliers final: 89 residues processed: 394 average time/residue: 0.9779 time to fit residues: 484.6270 Evaluate side-chains 331 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 236 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 62 ARG Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 88 TYR Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 88 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 124 optimal weight: 2.9990 chunk 333 optimal weight: 30.0000 chunk 73 optimal weight: 0.3980 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 370 optimal weight: 7.9990 chunk 307 optimal weight: 0.9980 chunk 171 optimal weight: 0.0970 chunk 30 optimal weight: 0.3980 chunk 122 optimal weight: 0.5980 chunk 194 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 755 GLN B1106 GLN C 196 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 949 GLN ** R 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31558 Z= 0.203 Angle : 0.650 11.711 42932 Z= 0.330 Chirality : 0.048 0.432 4983 Planarity : 0.005 0.056 5487 Dihedral : 6.758 58.967 5370 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 3.61 % Allowed : 19.42 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 3814 helix: 1.78 (0.20), residues: 666 sheet: -0.57 (0.16), residues: 994 loop : -1.45 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP T 47 HIS 0.019 0.001 HIS B1058 PHE 0.048 0.002 PHE Q 63 TYR 0.031 0.001 TYR O 50 ARG 0.007 0.000 ARG T 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 243 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7310 (mt) REVERT: B 180 GLU cc_start: 0.1638 (OUTLIER) cc_final: -0.0189 (mt-10) REVERT: B 218 GLN cc_start: 0.1967 (OUTLIER) cc_final: -0.0006 (pm20) REVERT: B 577 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.5268 (ptp90) REVERT: B 762 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.6307 (tm-30) REVERT: B 1106 GLN cc_start: 0.6497 (OUTLIER) cc_final: 0.6296 (tt0) REVERT: B 1113 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6670 (mt0) REVERT: C 177 MET cc_start: 0.1680 (ttt) cc_final: 0.0764 (mpt) REVERT: C 374 PHE cc_start: 0.7245 (m-80) cc_final: 0.6825 (m-80) REVERT: C 780 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6070 (pp20) REVERT: C 1113 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: R 48 MET cc_start: 0.7538 (ptp) cc_final: 0.7149 (mpp) REVERT: R 54 MET cc_start: 0.6707 (mpp) cc_final: 0.6096 (mpp) REVERT: R 81 MET cc_start: 0.0459 (mmm) cc_final: 0.0084 (mmm) REVERT: T 39 GLN cc_start: 0.7883 (mt0) cc_final: 0.7254 (mm110) REVERT: T 48 MET cc_start: 0.7652 (mmm) cc_final: 0.7312 (mpt) REVERT: T 70 PHE cc_start: 0.7371 (m-10) cc_final: 0.6893 (m-80) REVERT: T 83 LEU cc_start: 0.8288 (pt) cc_final: 0.7843 (tm) REVERT: T 90 ASP cc_start: 0.7770 (m-30) cc_final: 0.7476 (m-30) REVERT: T 118 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7570 (mm) REVERT: Q 88 TYR cc_start: 0.7586 (m-80) cc_final: 0.7259 (m-80) REVERT: K 54 MET cc_start: 0.3394 (OUTLIER) cc_final: 0.2828 (pmt) REVERT: K 60 TYR cc_start: 0.3811 (OUTLIER) cc_final: 0.3509 (t80) REVERT: K 102 TYR cc_start: 0.0749 (m-80) cc_final: 0.0267 (m-80) outliers start: 120 outliers final: 64 residues processed: 337 average time/residue: 1.0426 time to fit residues: 439.1766 Evaluate side-chains 298 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 222 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain R residue 29 PHE Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain O residue 62 ARG Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 88 TYR Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 24 ARG Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 357 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 211 optimal weight: 0.1980 chunk 270 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 chunk 311 optimal weight: 0.6980 chunk 206 optimal weight: 0.6980 chunk 369 optimal weight: 0.3980 chunk 231 optimal weight: 3.9990 chunk 225 optimal weight: 20.0000 chunk 170 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B1106 GLN C 493 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** R 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31558 Z= 0.220 Angle : 0.648 11.538 42932 Z= 0.330 Chirality : 0.048 0.425 4983 Planarity : 0.004 0.086 5487 Dihedral : 6.589 59.788 5369 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 3.82 % Allowed : 19.66 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 3814 helix: 1.88 (0.20), residues: 665 sheet: -0.51 (0.16), residues: 1012 loop : -1.43 (0.12), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 104 HIS 0.002 0.001 HIS C 245 PHE 0.049 0.002 PHE Q 63 TYR 0.023 0.001 TYR C 505 ARG 0.012 0.000 ARG T 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 241 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.3467 (OUTLIER) cc_final: 0.3261 (t80) REVERT: B 180 GLU cc_start: 0.1896 (OUTLIER) cc_final: -0.0036 (mt-10) REVERT: B 218 GLN cc_start: 0.1764 (OUTLIER) cc_final: 0.0043 (pm20) REVERT: B 577 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.5277 (ptp90) REVERT: B 762 GLN cc_start: 0.6589 (OUTLIER) cc_final: 0.6329 (tm-30) REVERT: C 177 MET cc_start: 0.1603 (ttt) cc_final: 0.0622 (mpt) REVERT: C 780 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6143 (pp20) REVERT: C 1113 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6886 (mp10) REVERT: R 48 MET cc_start: 0.7550 (ptp) cc_final: 0.7248 (mpp) REVERT: R 54 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6100 (mpp) REVERT: R 81 MET cc_start: 0.0406 (mmm) cc_final: 0.0104 (mmm) REVERT: T 39 GLN cc_start: 0.7832 (mt0) cc_final: 0.7463 (mm110) REVERT: T 118 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7518 (mm) REVERT: K 48 MET cc_start: 0.3122 (pmm) cc_final: 0.2749 (pmt) REVERT: K 60 TYR cc_start: 0.3866 (OUTLIER) cc_final: 0.3509 (t80) REVERT: K 102 TYR cc_start: 0.1135 (m-80) cc_final: 0.0285 (m-80) outliers start: 127 outliers final: 85 residues processed: 335 average time/residue: 0.9860 time to fit residues: 420.5445 Evaluate side-chains 319 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 224 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain R residue 29 PHE Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 62 ARG Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 88 TYR Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 88 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 228 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 220 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 234 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 290 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 703 ASN B1058 HIS ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31558 Z= 0.258 Angle : 0.670 17.932 42932 Z= 0.342 Chirality : 0.049 0.415 4983 Planarity : 0.005 0.058 5487 Dihedral : 6.509 59.713 5369 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 3.88 % Allowed : 19.81 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 3814 helix: 1.74 (0.20), residues: 678 sheet: -0.54 (0.16), residues: 1019 loop : -1.42 (0.12), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP O 36 HIS 0.003 0.001 HIS B1058 PHE 0.046 0.002 PHE Q 63 TYR 0.025 0.002 TYR C 200 ARG 0.013 0.001 ARG T 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 238 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.2747 (ttt) cc_final: 0.2498 (ttt) REVERT: B 180 GLU cc_start: 0.2054 (OUTLIER) cc_final: 0.0022 (mt-10) REVERT: B 218 GLN cc_start: 0.1635 (OUTLIER) cc_final: -0.0219 (pm20) REVERT: B 577 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.5299 (ptp90) REVERT: B 814 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.6108 (mmmt) REVERT: B 1113 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6662 (mt0) REVERT: C 177 MET cc_start: 0.1552 (ttt) cc_final: 0.0920 (mpt) REVERT: C 780 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6194 (pp20) REVERT: R 7 SER cc_start: -0.0092 (OUTLIER) cc_final: -0.0461 (m) REVERT: R 48 MET cc_start: 0.7594 (ptp) cc_final: 0.7324 (mpp) REVERT: R 54 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6359 (mpp) REVERT: R 81 MET cc_start: 0.0398 (mmm) cc_final: 0.0132 (mmm) REVERT: O 48 LEU cc_start: 0.8406 (pp) cc_final: 0.7974 (pt) REVERT: T 39 GLN cc_start: 0.7957 (mt0) cc_final: 0.7294 (tp40) REVERT: T 45 LEU cc_start: 0.8188 (mp) cc_final: 0.7922 (mp) REVERT: T 54 MET cc_start: 0.7593 (mpt) cc_final: 0.7290 (mpt) REVERT: T 118 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7384 (mm) REVERT: K 60 TYR cc_start: 0.3905 (OUTLIER) cc_final: 0.3615 (t80) REVERT: K 102 TYR cc_start: 0.0959 (m-80) cc_final: 0.0220 (m-80) outliers start: 129 outliers final: 87 residues processed: 336 average time/residue: 1.0105 time to fit residues: 425.5014 Evaluate side-chains 318 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 221 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 29 PHE Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 62 ARG Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 88 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.2145 > 50: distance: 66 - 91: 3.926 distance: 88 - 89: 3.566 distance: 89 - 92: 3.258 distance: 90 - 91: 3.856 distance: 93 - 94: 3.556 distance: 94 - 95: 3.121 distance: 95 - 102: 3.735 distance: 99 - 100: 3.378 distance: 102 - 103: 4.440 distance: 104 - 105: 4.046 distance: 106 - 107: 5.503 distance: 107 - 108: 4.428 distance: 108 - 110: 6.377 distance: 112 - 115: 4.281 distance: 115 - 116: 4.898 distance: 118 - 119: 4.967 distance: 129 - 130: 3.724 distance: 129 - 132: 3.029 distance: 130 - 131: 5.540 distance: 133 - 134: 4.892 distance: 133 - 135: 3.142 distance: 134 - 136: 3.506 distance: 135 - 137: 3.250 distance: 136 - 138: 3.914 distance: 139 - 140: 4.036 distance: 140 - 141: 4.171 distance: 141 - 142: 3.076 distance: 142 - 194: 11.822 distance: 143 - 145: 5.265 distance: 146 - 147: 7.926 distance: 147 - 148: 14.346 distance: 147 - 150: 9.429 distance: 148 - 149: 15.406 distance: 148 - 153: 13.554 distance: 150 - 151: 7.183 distance: 150 - 152: 5.491 distance: 153 - 154: 8.886 distance: 154 - 155: 16.517 distance: 154 - 157: 20.489 distance: 155 - 156: 26.481 distance: 155 - 158: 6.352 distance: 158 - 159: 3.014 distance: 158 - 164: 3.880 distance: 159 - 160: 3.229 distance: 159 - 162: 3.572 distance: 163 - 164: 3.030