Starting phenix.real_space_refine on Tue Aug 26 18:29:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kms_22927/08_2025/7kms_22927.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kms_22927/08_2025/7kms_22927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kms_22927/08_2025/7kms_22927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kms_22927/08_2025/7kms_22927.map" model { file = "/net/cci-nas-00/data/ceres_data/7kms_22927/08_2025/7kms_22927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kms_22927/08_2025/7kms_22927.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 198 5.16 5 C 25305 2.51 5 N 6490 2.21 5 O 7684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 230 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39677 Number of models: 1 Model: "" Number of chains: 20 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "A" Number of atoms: 8033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8033 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 8033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8033 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 8031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8031 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "C" 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: 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: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.97, per 1000 atoms: 0.20 Number of scatterers: 39677 At special positions: 0 Unit cell: (161.874, 175.628, 239.108, 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 198 16.00 O 7684 8.00 N 6490 7.00 C 25305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.06 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 K 1 " - " NAG K 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 331 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 234 " " NAG A1311 " - " ASN A 603 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN B 603 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 343 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 343 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 90 " " NAG D 705 " - " ASN D 53 " " NAG E 701 " - " ASN E 546 " " NAG E 702 " - " ASN E 322 " " NAG E 703 " - " ASN E 432 " " NAG E 704 " - " ASN E 103 " " NAG E 705 " - " ASN E 90 " " NAG E 706 " - " ASN E 53 " " NAG F 701 " - " ASN F 322 " " NAG F 702 " - " ASN F 432 " " NAG F 703 " - " ASN F 103 " " NAG F 704 " - " ASN F 90 " " NAG F 705 " - " ASN F 53 " " NAG G 1 " - " ASN F 546 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN C1134 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN D 546 " Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9198 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 48 sheets defined 38.7% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'F' and resid 20 through 51 removed outlier: 3.523A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 82 removed outlier: 3.511A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.524A pdb=" N LYS F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 128 removed outlier: 4.362A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 Processing helix chain 'F' and resid 149 through 154 removed outlier: 3.835A pdb=" N ASN F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 170 removed outlier: 3.683A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 176 through 194 removed outlier: 3.623A pdb=" N GLU F 181 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 186 " --> pdb=" O GLU F 182 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 206 removed outlier: 3.545A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP F 203 " --> pdb=" O TYR F 199 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG F 204 " --> pdb=" O GLY F 200 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP F 206 " --> pdb=" O TYR F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 249 removed outlier: 3.765A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.605A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 277 through 282 removed outlier: 4.459A pdb=" N LEU F 281 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 301 removed outlier: 3.812A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.865A pdb=" N PHE F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL F 316 " --> pdb=" O GLU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 4.081A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE F 379 " --> pdb=" O GLU F 375 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET F 383 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA F 384 " --> pdb=" O GLN F 380 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 413 removed outlier: 3.766A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER F 411 " --> pdb=" O ILE F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.515A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 466 removed outlier: 4.561A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.700A pdb=" N LYS F 476 " --> pdb=" O GLN F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 523 removed outlier: 4.167A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 533 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.718A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.540A pdb=" N ALA F 569 " --> pdb=" O PRO F 565 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 570 " --> pdb=" O TRP F 566 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 565 through 572' Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 588 through 599 Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.566A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.679A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.613A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.459A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.309A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.722A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.673A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.908A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.676A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 937 removed outlier: 3.699A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 966 removed outlier: 4.367A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.617A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.045A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 3.735A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.654A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.626A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.409A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 390' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.740A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.750A pdb=" N VAL C 622 " --> pdb=" O GLU C 619 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 623 " --> pdb=" O VAL C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 619 through 623' Processing helix chain 'C' and resid 738 through 743 removed outlier: 3.961A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.679A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.885A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.577A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.558A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 938 removed outlier: 3.683A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 4.283A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN C 953 " --> pdb=" O GLN C 949 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.573A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.032A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 3.969A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.558A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.533A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.092A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.483A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 738 through 743 removed outlier: 4.054A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.008A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.607A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.629A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.098A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.585A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.349A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.504A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 4.274A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.596A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.021A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.017A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 3.520A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.550A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.721A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 removed outlier: 4.107A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET D 123 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 149 removed outlier: 3.821A pdb=" N GLY D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.755A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 176 through 187 removed outlier: 3.679A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 3.645A pdb=" N ALA D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.509A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.710A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.539A pdb=" N ALA D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 277 through 282 removed outlier: 4.371A pdb=" N LEU D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 removed outlier: 3.679A pdb=" N MET D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.634A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.580A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET D 383 " --> pdb=" O ILE D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 399 through 404 Processing helix chain 'D' and resid 406 through 413 removed outlier: 3.555A pdb=" N LEU D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.500A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.513A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.622A pdb=" N TRP D 477 " --> pdb=" O TRP D 473 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.024A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.591A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.505A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 removed outlier: 4.079A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 581 through 586' Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.509A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 51 removed outlier: 3.515A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 82 removed outlier: 3.705A pdb=" N VAL E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.628A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 removed outlier: 4.264A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 154 removed outlier: 4.091A pdb=" N ASN E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 170 removed outlier: 3.758A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 187 removed outlier: 3.782A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 194 removed outlier: 3.547A pdb=" N ALA E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 220 through 249 removed outlier: 3.897A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 280 removed outlier: 4.110A pdb=" N SER E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.545A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.634A pdb=" N ALA E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.607A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY E 377 " --> pdb=" O HIS E 373 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 405 removed outlier: 3.790A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 413 Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.575A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 removed outlier: 3.827A pdb=" N GLY E 466 " --> pdb=" O MET E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.758A pdb=" N LYS E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP E 477 " --> pdb=" O TRP E 473 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 3.942A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.716A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.557A pdb=" N LEU E 570 " --> pdb=" O TRP E 566 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 586 removed outlier: 4.293A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN E 586 " --> pdb=" O ARG E 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 581 through 586' Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.614A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.832A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 347 through 352 removed outlier: 3.523A pdb=" N LEU F 359 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG F 357 " --> pdb=" O TRP F 349 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.541A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 210 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.095A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.728A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.824A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.972A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.248A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 380 removed outlier: 3.609A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (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 538 through 542 removed outlier: 3.881A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.529A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.807A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.807A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.201A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.359A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.796A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.718A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.175A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.292A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 318 removed outlier: 7.192A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.897A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 660 removed outlier: 3.633A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.505A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.505A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.251A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD4, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.683A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.505A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.110A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.369A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.297A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.980A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.370A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.749A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.749A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.210A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.036A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.445A pdb=" N ALA D 348 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU D 359 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP D 350 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ARG D 357 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.032A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 347 through 352 removed outlier: 5.809A pdb=" N ALA E 348 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU E 359 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP E 350 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ARG E 357 " --> pdb=" O ASP E 350 " (cutoff:3.500A) 1505 hydrogen bonds defined for protein. 4266 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: 8.44 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 12645 1.35 - 1.47: 10543 1.47 - 1.60: 17158 1.60 - 1.72: 0 1.72 - 1.85: 291 Bond restraints: 40637 Sorted by residual: bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 40632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 53719 1.29 - 2.59: 1171 2.59 - 3.88: 295 3.88 - 5.17: 72 5.17 - 6.47: 6 Bond angle restraints: 55263 Sorted by residual: angle pdb=" N LEU C 335 " pdb=" CA LEU C 335 " pdb=" C LEU C 335 " ideal model delta sigma weight residual 107.73 111.58 -3.85 1.34e+00 5.57e-01 8.26e+00 angle pdb=" N VAL F 185 " pdb=" CA VAL F 185 " pdb=" C VAL F 185 " ideal model delta sigma weight residual 111.81 109.40 2.41 8.60e-01 1.35e+00 7.83e+00 angle pdb=" N VAL D 185 " pdb=" CA VAL D 185 " pdb=" C VAL D 185 " ideal model delta sigma weight residual 111.81 109.45 2.36 8.60e-01 1.35e+00 7.50e+00 angle pdb=" N VAL A1033 " pdb=" CA VAL A1033 " pdb=" C VAL A1033 " ideal model delta sigma weight residual 111.48 108.95 2.53 9.40e-01 1.13e+00 7.25e+00 angle pdb=" N LYS C 529 " pdb=" CA LYS C 529 " pdb=" C LYS C 529 " ideal model delta sigma weight residual 110.80 116.03 -5.23 2.13e+00 2.20e-01 6.03e+00 ... (remaining 55258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 22533 17.77 - 35.53: 2016 35.53 - 53.30: 396 53.30 - 71.06: 83 71.06 - 88.83: 29 Dihedral angle restraints: 25057 sinusoidal: 10783 harmonic: 14274 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -0.49 -85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 11.23 81.77 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 36.41 56.59 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 25054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4982 0.042 - 0.084: 798 0.084 - 0.125: 497 0.125 - 0.167: 29 0.167 - 0.209: 2 Chirality restraints: 6308 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA VAL B 130 " pdb=" N VAL B 130 " pdb=" C VAL B 130 " pdb=" CB VAL B 130 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 6305 not shown) Planarity restraints: 7120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO C 987 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 987 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO C 337 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " -0.029 5.00e-02 4.00e+02 ... (remaining 7117 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 627 2.64 - 3.21: 37706 3.21 - 3.77: 60344 3.77 - 4.34: 83042 4.34 - 4.90: 134246 Nonbonded interactions: 315965 Sorted by model distance: nonbonded pdb=" O PHE B1089 " pdb=" OG1 THR B1120 " model vdw 2.079 3.040 nonbonded pdb=" NZ LYS C 129 " pdb=" OE1 GLU C 169 " model vdw 2.131 3.120 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.159 3.040 nonbonded pdb=" OH TYR E 217 " pdb=" OD2 ASP E 225 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASN C 540 " pdb=" OG1 THR C 549 " model vdw 2.178 3.040 ... (remaining 315960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 675 or resid 691 through 1313)) selection = (chain 'B' and (resid 26 through 675 or resid 691 through 1313)) selection = (chain 'C' and (resid 26 through 675 or resid 691 through 1313)) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 19 through 705) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 32.760 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.080 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40756 Z= 0.145 Angle : 0.508 6.466 55572 Z= 0.250 Chirality : 0.041 0.209 6308 Planarity : 0.003 0.057 7057 Dihedral : 13.847 88.830 15715 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.13), residues: 4833 helix: 1.22 (0.14), residues: 1522 sheet: 0.52 (0.21), residues: 616 loop : -0.80 (0.12), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 328 TYR 0.010 0.001 TYR E 510 PHE 0.010 0.001 PHE C 338 TRP 0.007 0.001 TRP C 886 HIS 0.004 0.000 HIS E 540 Details of bonding type rmsd covalent geometry : bond 0.00301 (40637) covalent geometry : angle 0.50258 (55263) SS BOND : bond 0.00504 ( 48) SS BOND : angle 0.95397 ( 96) hydrogen bonds : bond 0.27834 ( 1471) hydrogen bonds : angle 8.43372 ( 4266) link_BETA1-4 : bond 0.00249 ( 8) link_BETA1-4 : angle 0.94891 ( 24) link_NAG-ASN : bond 0.00150 ( 63) link_NAG-ASN : angle 1.26052 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: F 249 MET cc_start: 0.6695 (mmp) cc_final: 0.6439 (mmp) REVERT: F 383 MET cc_start: 0.8955 (mpp) cc_final: 0.8659 (mpp) REVERT: C 153 MET cc_start: 0.3107 (ppp) cc_final: 0.2470 (tmm) REVERT: B 1050 MET cc_start: 0.8407 (pmm) cc_final: 0.8065 (pmm) REVERT: E 376 MET cc_start: 0.7869 (mpp) cc_final: 0.7486 (mpp) REVERT: E 383 MET cc_start: 0.8760 (mpp) cc_final: 0.8527 (mpp) REVERT: E 557 MET cc_start: 0.7994 (ppp) cc_final: 0.7583 (ppp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2056 time to fit residues: 52.4269 Evaluate side-chains 123 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0470 chunk 207 optimal weight: 0.0570 chunk 470 optimal weight: 30.0000 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 373 HIS F 374 HIS A 52 GLN A 394 ASN A 901 GLN B 52 GLN B 121 ASN B 394 ASN B 580 GLN D 188 ASN D 373 HIS D 472 GLN E 188 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.071778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.047631 restraints weight = 300477.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.047352 restraints weight = 166006.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.047452 restraints weight = 105957.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.047450 restraints weight = 66748.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.047551 restraints weight = 62079.986| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 40756 Z= 0.185 Angle : 0.595 8.699 55572 Z= 0.306 Chirality : 0.044 0.241 6308 Planarity : 0.004 0.060 7057 Dihedral : 6.125 59.880 6720 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.31 % Allowed : 6.02 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.12), residues: 4833 helix: 0.67 (0.13), residues: 1622 sheet: -0.11 (0.19), residues: 692 loop : -1.11 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 328 TYR 0.020 0.001 TYR C 904 PHE 0.023 0.001 PHE F 512 TRP 0.013 0.001 TRP D 271 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00396 (40637) covalent geometry : angle 0.58715 (55263) SS BOND : bond 0.00372 ( 48) SS BOND : angle 1.17453 ( 96) hydrogen bonds : bond 0.05229 ( 1471) hydrogen bonds : angle 5.64686 ( 4266) link_BETA1-4 : bond 0.00694 ( 8) link_BETA1-4 : angle 1.24640 ( 24) link_NAG-ASN : bond 0.00291 ( 63) link_NAG-ASN : angle 1.52599 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: -0.0962 (tpp) cc_final: -0.1657 (tpt) REVERT: C 153 MET cc_start: 0.3367 (ppp) cc_final: 0.2913 (tmm) REVERT: B 1029 MET cc_start: 0.9262 (tpp) cc_final: 0.8927 (tpp) REVERT: B 1050 MET cc_start: 0.8676 (pmm) cc_final: 0.8166 (ptp) REVERT: D 123 MET cc_start: 0.3474 (mpp) cc_final: 0.3258 (mpp) REVERT: D 152 MET cc_start: -0.0282 (tpp) cc_final: -0.0522 (ttm) REVERT: D 190 MET cc_start: 0.3792 (ppp) cc_final: 0.3298 (ppp) REVERT: D 249 MET cc_start: 0.4193 (mmt) cc_final: 0.2788 (mtt) REVERT: D 270 MET cc_start: 0.0933 (ppp) cc_final: 0.0476 (ppp) REVERT: D 408 MET cc_start: 0.7260 (pmm) cc_final: 0.6983 (pmm) REVERT: E 376 MET cc_start: 0.8362 (mpp) cc_final: 0.8100 (mpt) REVERT: E 383 MET cc_start: 0.9111 (mpp) cc_final: 0.8869 (mpp) outliers start: 13 outliers final: 3 residues processed: 141 average time/residue: 0.2218 time to fit residues: 55.9835 Evaluate side-chains 122 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain C residue 759 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 315 optimal weight: 0.6980 chunk 295 optimal weight: 0.1980 chunk 274 optimal weight: 8.9990 chunk 335 optimal weight: 0.9980 chunk 473 optimal weight: 20.0000 chunk 240 optimal weight: 0.9990 chunk 327 optimal weight: 0.9990 chunk 6 optimal weight: 0.0060 chunk 8 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 428 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 374 HIS E 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.072761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.049994 restraints weight = 307379.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.049597 restraints weight = 179186.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.049481 restraints weight = 132890.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.049781 restraints weight = 96247.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.049712 restraints weight = 84039.975| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 40756 Z= 0.101 Angle : 0.497 7.764 55572 Z= 0.255 Chirality : 0.042 0.199 6308 Planarity : 0.003 0.068 7057 Dihedral : 5.578 59.649 6720 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.26 % Allowed : 8.42 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.12), residues: 4833 helix: 0.70 (0.13), residues: 1636 sheet: -0.10 (0.19), residues: 705 loop : -1.11 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1014 TYR 0.014 0.001 TYR C 904 PHE 0.012 0.001 PHE F 512 TRP 0.010 0.001 TRP F 165 HIS 0.004 0.000 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00206 (40637) covalent geometry : angle 0.49054 (55263) SS BOND : bond 0.00327 ( 48) SS BOND : angle 0.77562 ( 96) hydrogen bonds : bond 0.04644 ( 1471) hydrogen bonds : angle 5.20994 ( 4266) link_BETA1-4 : bond 0.00385 ( 8) link_BETA1-4 : angle 0.98113 ( 24) link_NAG-ASN : bond 0.00247 ( 63) link_NAG-ASN : angle 1.31053 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: -0.1484 (tpp) cc_final: -0.1740 (tpt) REVERT: C 153 MET cc_start: 0.3252 (ppp) cc_final: 0.2853 (tmm) REVERT: B 1029 MET cc_start: 0.9103 (tpp) cc_final: 0.8813 (tpp) REVERT: B 1050 MET cc_start: 0.8568 (pmm) cc_final: 0.8208 (ptp) REVERT: D 123 MET cc_start: 0.3253 (mpp) cc_final: 0.3041 (mpp) REVERT: D 133 CYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7253 (t) REVERT: D 190 MET cc_start: 0.3901 (ppp) cc_final: 0.3417 (ppp) REVERT: D 249 MET cc_start: 0.3293 (mmt) cc_final: 0.1604 (mtt) REVERT: D 408 MET cc_start: 0.7357 (pmm) cc_final: 0.7072 (pmm) REVERT: E 376 MET cc_start: 0.8307 (mpp) cc_final: 0.7987 (mpp) REVERT: E 383 MET cc_start: 0.9077 (mpp) cc_final: 0.8829 (mpp) outliers start: 11 outliers final: 3 residues processed: 138 average time/residue: 0.1847 time to fit residues: 45.0952 Evaluate side-chains 123 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 121 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 438 optimal weight: 30.0000 chunk 404 optimal weight: 30.0000 chunk 205 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 469 optimal weight: 6.9990 chunk 153 optimal weight: 0.5980 chunk 193 optimal weight: 9.9990 chunk 105 optimal weight: 0.0020 chunk 210 optimal weight: 3.9990 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 277 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.072051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.048374 restraints weight = 301112.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.047810 restraints weight = 175694.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.047894 restraints weight = 112902.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.048481 restraints weight = 80729.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.048328 restraints weight = 65628.524| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40756 Z= 0.122 Angle : 0.499 8.063 55572 Z= 0.253 Chirality : 0.042 0.216 6308 Planarity : 0.003 0.067 7057 Dihedral : 5.166 58.896 6720 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.42 % Allowed : 9.86 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.12), residues: 4833 helix: 0.78 (0.13), residues: 1641 sheet: -0.19 (0.19), residues: 705 loop : -1.11 (0.12), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 102 TYR 0.012 0.001 TYR A1067 PHE 0.012 0.001 PHE B 392 TRP 0.010 0.001 TRP F 165 HIS 0.003 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00264 (40637) covalent geometry : angle 0.49228 (55263) SS BOND : bond 0.00244 ( 48) SS BOND : angle 0.74173 ( 96) hydrogen bonds : bond 0.03905 ( 1471) hydrogen bonds : angle 4.90133 ( 4266) link_BETA1-4 : bond 0.00208 ( 8) link_BETA1-4 : angle 1.04024 ( 24) link_NAG-ASN : bond 0.00186 ( 63) link_NAG-ASN : angle 1.38443 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 249 MET cc_start: 0.7005 (mmp) cc_final: 0.6659 (mmp) REVERT: F 323 MET cc_start: -0.1391 (tpp) cc_final: -0.1717 (tpt) REVERT: A 323 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8816 (p) REVERT: C 153 MET cc_start: 0.3373 (ppp) cc_final: 0.2969 (tmm) REVERT: C 1050 MET cc_start: 0.8826 (ptt) cc_final: 0.8622 (ptt) REVERT: B 195 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8634 (ptpp) REVERT: B 1029 MET cc_start: 0.9162 (tpp) cc_final: 0.8840 (tpp) REVERT: D 133 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6712 (t) REVERT: D 190 MET cc_start: 0.3708 (ppp) cc_final: 0.3237 (ppp) REVERT: D 249 MET cc_start: 0.3331 (mmt) cc_final: 0.1396 (mtt) REVERT: E 332 MET cc_start: 0.6583 (tmm) cc_final: 0.6368 (tmm) REVERT: E 376 MET cc_start: 0.8324 (mpp) cc_final: 0.8033 (mpp) REVERT: E 383 MET cc_start: 0.9066 (mpp) cc_final: 0.8817 (mpp) REVERT: E 462 MET cc_start: 0.8521 (ppp) cc_final: 0.8110 (mmt) outliers start: 18 outliers final: 6 residues processed: 140 average time/residue: 0.2129 time to fit residues: 52.7586 Evaluate side-chains 130 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 117 optimal weight: 8.9990 chunk 337 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 268 optimal weight: 4.9990 chunk 343 optimal weight: 0.6980 chunk 461 optimal weight: 10.0000 chunk 458 optimal weight: 0.8980 chunk 466 optimal weight: 20.0000 chunk 249 optimal weight: 4.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.070450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.045887 restraints weight = 313228.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.046400 restraints weight = 154004.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.047265 restraints weight = 87729.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.046807 restraints weight = 86509.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.046810 restraints weight = 70430.446| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 40756 Z= 0.218 Angle : 0.593 17.512 55572 Z= 0.300 Chirality : 0.043 0.255 6308 Planarity : 0.004 0.067 7057 Dihedral : 5.298 59.811 6720 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.20 % Allowed : 10.99 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.12), residues: 4833 helix: 0.72 (0.13), residues: 1679 sheet: -0.45 (0.19), residues: 688 loop : -1.21 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 102 TYR 0.013 0.001 TYR C 904 PHE 0.017 0.002 PHE C1042 TRP 0.014 0.001 TRP C 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00469 (40637) covalent geometry : angle 0.58336 (55263) SS BOND : bond 0.00420 ( 48) SS BOND : angle 1.11039 ( 96) hydrogen bonds : bond 0.03858 ( 1471) hydrogen bonds : angle 4.95337 ( 4266) link_BETA1-4 : bond 0.00278 ( 8) link_BETA1-4 : angle 1.28716 ( 24) link_NAG-ASN : bond 0.00296 ( 63) link_NAG-ASN : angle 1.70897 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: -0.0783 (tpp) cc_final: -0.1036 (tpt) REVERT: A 33 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8674 (p) REVERT: A 323 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8848 (p) REVERT: A 1031 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: C 153 MET cc_start: 0.3414 (ppp) cc_final: 0.3117 (tmm) REVERT: C 697 MET cc_start: 0.8641 (mmm) cc_final: 0.8336 (tpp) REVERT: C 1031 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: B 195 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8624 (pttt) REVERT: B 323 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8718 (p) REVERT: B 1029 MET cc_start: 0.9268 (tpp) cc_final: 0.8913 (tpp) REVERT: B 1031 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: B 1050 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8420 (ptp) REVERT: D 123 MET cc_start: 0.2274 (mpp) cc_final: 0.1741 (mtt) REVERT: D 133 CYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7274 (t) REVERT: D 152 MET cc_start: -0.0288 (tpp) cc_final: -0.0510 (ttm) REVERT: D 190 MET cc_start: 0.4229 (ppp) cc_final: 0.3722 (ppp) REVERT: D 249 MET cc_start: 0.3318 (mmt) cc_final: 0.1601 (mtt) REVERT: D 408 MET cc_start: 0.7638 (pmm) cc_final: 0.7434 (pmm) REVERT: E 376 MET cc_start: 0.8360 (mpp) cc_final: 0.8102 (mpt) outliers start: 51 outliers final: 16 residues processed: 165 average time/residue: 0.1935 time to fit residues: 57.6656 Evaluate side-chains 138 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 42 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 466 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 261 optimal weight: 0.0870 chunk 234 optimal weight: 0.7980 chunk 406 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 402 optimal weight: 5.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B1083 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.071148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.046269 restraints weight = 308772.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.046981 restraints weight = 131665.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.047233 restraints weight = 81828.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.047313 restraints weight = 51686.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.047408 restraints weight = 45645.409| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 40756 Z= 0.124 Angle : 0.517 9.784 55572 Z= 0.261 Chirality : 0.042 0.223 6308 Planarity : 0.004 0.067 7057 Dihedral : 5.083 59.167 6720 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.92 % Allowed : 11.88 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.12), residues: 4833 helix: 0.84 (0.13), residues: 1658 sheet: -0.40 (0.19), residues: 688 loop : -1.16 (0.12), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 328 TYR 0.013 0.001 TYR B1067 PHE 0.011 0.001 PHE E 523 TRP 0.016 0.001 TRP E 461 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00273 (40637) covalent geometry : angle 0.50900 (55263) SS BOND : bond 0.00376 ( 48) SS BOND : angle 1.07940 ( 96) hydrogen bonds : bond 0.03496 ( 1471) hydrogen bonds : angle 4.74784 ( 4266) link_BETA1-4 : bond 0.00228 ( 8) link_BETA1-4 : angle 0.95817 ( 24) link_NAG-ASN : bond 0.00197 ( 63) link_NAG-ASN : angle 1.50884 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 249 MET cc_start: 0.7624 (mmp) cc_final: 0.6907 (mmp) REVERT: F 323 MET cc_start: -0.0638 (tpp) cc_final: -0.0944 (tpt) REVERT: A 33 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8639 (p) REVERT: A 323 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8821 (p) REVERT: C 153 MET cc_start: 0.3143 (ppp) cc_final: 0.2801 (tmm) REVERT: C 697 MET cc_start: 0.8666 (mmm) cc_final: 0.8453 (tmm) REVERT: C 1031 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8328 (mp0) REVERT: B 323 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8688 (p) REVERT: B 781 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.9075 (p) REVERT: B 1029 MET cc_start: 0.9206 (tpp) cc_final: 0.8902 (tpp) REVERT: B 1050 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8530 (ptp) REVERT: D 133 CYS cc_start: 0.7628 (p) cc_final: 0.7159 (t) REVERT: D 152 MET cc_start: -0.0062 (tpp) cc_final: -0.0347 (ttm) REVERT: D 190 MET cc_start: 0.4672 (ppp) cc_final: 0.4137 (ppp) REVERT: E 270 MET cc_start: 0.2425 (ttm) cc_final: 0.1481 (mtp) REVERT: E 383 MET cc_start: 0.9099 (mpp) cc_final: 0.8869 (mpp) outliers start: 39 outliers final: 17 residues processed: 151 average time/residue: 0.2077 time to fit residues: 56.6942 Evaluate side-chains 140 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 33 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 373 optimal weight: 9.9990 chunk 311 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 347 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 194 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN E 64 ASN E 373 HIS ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.070523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.045650 restraints weight = 311614.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.046374 restraints weight = 136371.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.046450 restraints weight = 80579.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.046702 restraints weight = 52078.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.046705 restraints weight = 46721.102| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 40756 Z= 0.174 Angle : 0.549 9.587 55572 Z= 0.276 Chirality : 0.042 0.239 6308 Planarity : 0.004 0.067 7057 Dihedral : 5.085 59.918 6720 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.01 % Allowed : 12.35 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.12), residues: 4833 helix: 0.87 (0.13), residues: 1662 sheet: -0.47 (0.19), residues: 678 loop : -1.14 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 102 TYR 0.013 0.001 TYR A1067 PHE 0.012 0.001 PHE E 523 TRP 0.016 0.001 TRP E 459 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00380 (40637) covalent geometry : angle 0.53954 (55263) SS BOND : bond 0.00463 ( 48) SS BOND : angle 1.20403 ( 96) hydrogen bonds : bond 0.03503 ( 1471) hydrogen bonds : angle 4.75449 ( 4266) link_BETA1-4 : bond 0.00231 ( 8) link_BETA1-4 : angle 0.99576 ( 24) link_NAG-ASN : bond 0.00230 ( 63) link_NAG-ASN : angle 1.66298 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9666 Ramachandran restraints generated. 4833 Oldfield, 0 Emsley, 4833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 39 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8316 (tp) REVERT: F 249 MET cc_start: 0.7642 (mmp) cc_final: 0.7326 (mmp) REVERT: F 323 MET cc_start: -0.0472 (tpp) cc_final: -0.0838 (tpt) REVERT: A 33 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8687 (p) REVERT: A 323 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8818 (p) REVERT: C 153 MET cc_start: 0.3191 (ppp) cc_final: 0.2946 (tmm) REVERT: C 697 MET cc_start: 0.8703 (mmm) cc_final: 0.8283 (tpt) REVERT: C 740 MET cc_start: 0.7719 (ppp) cc_final: 0.7436 (ppp) REVERT: C 1031 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: B 195 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8650 (pttm) REVERT: B 323 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8685 (p) REVERT: B 1029 MET cc_start: 0.9240 (tpp) cc_final: 0.8883 (tpp) REVERT: B 1050 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8454 (ptp) REVERT: D 133 CYS cc_start: 0.7623 (p) cc_final: 0.7134 (t) REVERT: D 152 MET cc_start: -0.0357 (tpp) cc_final: -0.0557 (ttm) REVERT: D 190 MET cc_start: 0.4812 (ppp) cc_final: 0.4243 (ppp) REVERT: E 383 MET cc_start: 0.9120 (mpp) cc_final: 0.8889 (mpp) outliers start: 43 outliers final: 26 residues processed: 155 average time/residue: 0.1948 time to fit residues: 54.6068 Evaluate side-chains 148 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 608 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.7359 > 50: distance: 80 - 174: 27.532 distance: 83 - 171: 30.106 distance: 141 - 145: 11.403 distance: 145 - 146: 17.458 distance: 146 - 147: 7.348 distance: 146 - 149: 24.253 distance: 147 - 148: 31.245 distance: 147 - 156: 10.609 distance: 150 - 151: 8.586 distance: 151 - 153: 18.961 distance: 153 - 155: 8.715 distance: 154 - 155: 18.683 distance: 156 - 157: 18.804 distance: 156 - 162: 17.673 distance: 157 - 158: 9.564 distance: 157 - 160: 14.122 distance: 158 - 159: 15.012 distance: 158 - 163: 16.829 distance: 160 - 161: 20.430 distance: 161 - 162: 6.762 distance: 163 - 164: 16.901 distance: 164 - 165: 13.933 distance: 164 - 167: 26.487 distance: 165 - 166: 11.364 distance: 165 - 171: 11.533 distance: 168 - 170: 24.226 distance: 171 - 172: 3.679 distance: 172 - 173: 18.417 distance: 172 - 175: 31.980 distance: 173 - 174: 33.938 distance: 173 - 180: 17.480 distance: 175 - 176: 13.356 distance: 176 - 177: 12.263 distance: 177 - 178: 22.120 distance: 177 - 179: 20.239 distance: 180 - 181: 26.411 distance: 181 - 182: 4.315 distance: 181 - 184: 17.365 distance: 182 - 183: 20.389 distance: 182 - 186: 3.409 distance: 184 - 185: 41.629 distance: 186 - 187: 3.072 distance: 187 - 188: 29.553 distance: 187 - 190: 18.998 distance: 188 - 189: 48.619 distance: 188 - 198: 12.375 distance: 190 - 191: 5.036 distance: 191 - 192: 30.526 distance: 191 - 193: 14.585 distance: 192 - 194: 13.932 distance: 194 - 196: 24.812 distance: 195 - 196: 21.905 distance: 200 - 201: 24.203 distance: 202 - 203: 3.393 distance: 203 - 204: 22.215 distance: 203 - 206: 22.439 distance: 204 - 205: 21.295 distance: 204 - 213: 19.296 distance: 206 - 207: 13.676 distance: 207 - 208: 16.506 distance: 207 - 209: 22.284 distance: 208 - 210: 19.525 distance: 209 - 211: 10.659 distance: 210 - 212: 5.668 distance: 213 - 214: 16.348 distance: 215 - 216: 3.611 distance: 215 - 222: 28.647 distance: 217 - 218: 30.233 distance: 219 - 220: 20.723 distance: 222 - 223: 5.661 distance: 222 - 228: 6.862 distance: 223 - 224: 22.476 distance: 223 - 226: 30.142 distance: 224 - 225: 20.535 distance: 224 - 229: 24.411 distance: 226 - 227: 21.893 distance: 227 - 228: 8.094