Starting phenix.real_space_refine on Thu Jan 15 13:49:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7my3_24078/01_2026/7my3_24078.cif Found real_map, /net/cci-nas-00/data/ceres_data/7my3_24078/01_2026/7my3_24078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7my3_24078/01_2026/7my3_24078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7my3_24078/01_2026/7my3_24078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7my3_24078/01_2026/7my3_24078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7my3_24078/01_2026/7my3_24078.map" } resolution = 2.9 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= 0.027 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 117 5.16 5 C 16657 2.51 5 N 4335 2.21 5 O 5117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26226 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7608 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 57, 'TRANS': 943} Chain breaks: 9 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASN:plan1': 7, 'PHE:plan': 5, 'GLU:plan': 7, 'TYR:plan': 2, 'ASP:plan': 10, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 151 Chain: "C" Number of atoms: 7190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7190 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'PTRANS': 55, 'TRANS': 952} Chain breaks: 6 Unresolved non-hydrogen bonds: 713 Unresolved non-hydrogen angles: 918 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'ASN:plan1': 17, 'GLU:plan': 15, 'ASP:plan': 17, 'GLN:plan1': 9, 'PHE:plan': 13, 'TYR:plan': 15, 'ARG:plan': 8, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 435 Chain: "B" Number of atoms: 7831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7831 Classifications: {'peptide': 1016} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 57, 'TRANS': 958} Chain breaks: 6 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 910 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "E" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 910 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 910 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" 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 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.16, per 1000 atoms: 0.23 Number of scatterers: 26226 At special positions: 0 Unit cell: (131.67, 141.075, 210.33, 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 117 16.00 O 5117 8.00 N 4335 7.00 C 16657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 32 " - pdb=" SG CYS H 100C" distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 100C" distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 32 " - pdb=" SG CYS D 100C" distance=2.04 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 F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 234 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 125 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 343 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 282 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN C 331 " " NAG M 1 " - " ASN C 343 " " NAG N 1 " - " ASN C 709 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN B 709 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B 331 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B1134 " Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 57 sheets defined 25.4% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.744A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.716A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.506A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.148A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.165A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.593A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.756A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.561A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 removed outlier: 4.089A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR A 827 " --> pdb=" O PHE A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.736A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.606A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.811A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.983A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.562A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.835A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1149 removed outlier: 4.409A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 4.075A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.658A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.752A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.595A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 638 removed outlier: 4.165A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.841A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.508A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.684A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.957A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.667A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.319A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.002A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.972A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.175A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.023A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.932A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.578A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.730A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.584A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.759A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.621A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.800A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 957 Processing helix chain 'B' and resid 959 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.514A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.331A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.515A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 31 removed outlier: 3.781A pdb=" N ASN H 30 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN H 31 " --> pdb=" O LEU H 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 26 through 31' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.811A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 31 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.598A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.374A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.067A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.362A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.925A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.874A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.897A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.831A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.708A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.887A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.403A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.729A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.729A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AC1, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.810A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.800A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.943A 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: 4.008A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AC6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.011A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.385A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.602A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.517A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.769A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.769A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'C' and resid 788 through 790 removed outlier: 5.454A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.177A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.820A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.037A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.852A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.406A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AE6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.347A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.665A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.519A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.768A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.545A pdb=" N LYS H 93 " --> pdb=" O ASP H 35 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA H 40 " --> pdb=" O GLU H 44 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.255A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER E 112 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL E 12 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 18 through 20 removed outlier: 3.538A pdb=" N LEU E 20 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 94 through 96 Processing sheet with id=AF9, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.604A pdb=" N SER D 7 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 82 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D 18 " --> pdb=" O MET D 82 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.604A pdb=" N SER D 7 " --> pdb=" O ILE D 21 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.131A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP D 35 " --> pdb=" O LYS D 93 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.131A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP D 35 " --> pdb=" O LYS D 93 " (cutoff:3.500A) 1078 hydrogen bonds defined for protein. 2874 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: 6.38 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8402 1.34 - 1.47: 6814 1.47 - 1.59: 11430 1.59 - 1.72: 0 1.72 - 1.84: 144 Bond restraints: 26790 Sorted by residual: bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.362 0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.30e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.16e+00 bond pdb=" N ALA A 123 " pdb=" CA ALA A 123 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.17e-02 7.31e+03 4.02e+00 ... (remaining 26785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 35544 2.18 - 4.35: 893 4.35 - 6.53: 89 6.53 - 8.71: 14 8.71 - 10.88: 2 Bond angle restraints: 36542 Sorted by residual: angle pdb=" CA ARG A 214 " pdb=" CB ARG A 214 " pdb=" CG ARG A 214 " ideal model delta sigma weight residual 114.10 124.98 -10.88 2.00e+00 2.50e-01 2.96e+01 angle pdb=" N ARG A 214 " pdb=" CA ARG A 214 " pdb=" CB ARG A 214 " ideal model delta sigma weight residual 113.89 106.83 7.06 1.93e+00 2.68e-01 1.34e+01 angle pdb=" N GLY B 482 " pdb=" CA GLY B 482 " pdb=" C GLY B 482 " ideal model delta sigma weight residual 114.95 110.13 4.82 1.41e+00 5.03e-01 1.17e+01 angle pdb=" N SER C 555 " pdb=" CA SER C 555 " pdb=" C SER C 555 " ideal model delta sigma weight residual 108.34 112.78 -4.44 1.31e+00 5.83e-01 1.15e+01 angle pdb=" C TYR B1067 " pdb=" N VAL B1068 " pdb=" CA VAL B1068 " ideal model delta sigma weight residual 122.85 119.94 2.91 8.70e-01 1.32e+00 1.12e+01 ... (remaining 36537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.46: 15756 22.46 - 44.91: 800 44.91 - 67.37: 122 67.37 - 89.82: 65 89.82 - 112.28: 24 Dihedral angle restraints: 16767 sinusoidal: 6965 harmonic: 9802 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 -178.00 -89.00 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.40 87.40 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -167.46 81.46 1 1.00e+01 1.00e-02 8.17e+01 ... (remaining 16764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.257: 4391 0.257 - 0.514: 6 0.514 - 0.771: 1 0.771 - 1.028: 0 1.028 - 1.285: 1 Chirality restraints: 4399 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-01 2.50e+01 4.13e+01 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" C4 NAG P 1 " pdb=" C3 NAG P 1 " pdb=" C5 NAG P 1 " pdb=" O4 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 4396 not shown) Planarity restraints: 4708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.034 2.00e-02 2.50e+03 3.09e-02 1.19e+01 pdb=" CG ASN A 61 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 64 " -0.024 2.00e-02 2.50e+03 1.80e-02 8.08e+00 pdb=" CG TRP A 64 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 64 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 64 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A 64 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 64 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 64 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 64 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 64 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 64 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " 0.019 2.00e-02 2.50e+03 2.04e-02 7.30e+00 pdb=" CG PHE C 906 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " 0.004 2.00e-02 2.50e+03 ... (remaining 4705 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 565 2.67 - 3.22: 24600 3.22 - 3.78: 37846 3.78 - 4.34: 49683 4.34 - 4.90: 85809 Nonbonded interactions: 198503 Sorted by model distance: nonbonded pdb=" NE2 GLN B 804 " pdb=" OE1 GLN B 935 " model vdw 2.108 3.120 nonbonded pdb=" OG SER B 359 " pdb=" OG1 THR B 523 " model vdw 2.135 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.135 3.040 nonbonded pdb=" O LEU C 293 " pdb=" OG1 THR C 632 " model vdw 2.151 3.040 nonbonded pdb=" O PHE B 329 " pdb=" NE2 GLN B 580 " model vdw 2.152 3.120 ... (remaining 198498 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 27 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 93 or (resid 94 through 100 and (n \ ame N or name CA or name C or name O or name CB )) or resid 101 through 107 or ( \ resid 108 through 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 119 or (resid 120 and (name N or name CA or name C or name O \ or name CB )) or resid 121 through 123 or (resid 124 through 129 and (name N or \ name CA or name C or name O or name CB )) or resid 130 through 133 or (resid 13 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 135 or (resi \ d 138 and (name N or name CA or name C or name O or name CB )) or resid 139 thro \ ugh 140 or resid 166 through 172 or (resid 187 through 190 and (name N or name C \ A or name C or name O or name CB )) or resid 191 through 204 or (resid 205 and ( \ name N or name CA or name C or name O or name CB )) or resid 206 through 207 or \ (resid 208 and (name N or name CA or name C or name O or name CB )) or resid 209 \ through 217 or (resid 218 and (name N or name CA or name C or name O or name CB \ )) or resid 219 through 220 or (resid 221 through 222 and (name N or name CA or \ name C or name O or name CB )) or resid 223 through 227 or (resid 228 through 2 \ 29 and (name N or name CA or name C or name O or name CB )) or resid 230 through \ 322 or (resid 323 through 324 and (name N or name CA or name C or name O or nam \ e CB )) or resid 325 through 331 or (resid 332 through 335 and (name N or name C \ A or name C or name O or name CB )) or resid 336 through 339 or (resid 340 throu \ gh 342 and (name N or name CA or name C or name O or name CB )) or resid 343 thr \ ough 348 or (resid 349 through 352 and (name N or name CA or name C or name O or \ name CB )) or resid 353 through 356 or (resid 357 and (name N or name CA or nam \ e C or name O or name CB )) or resid 358 or (resid 359 through 360 and (name N o \ r name CA or name C or name O or name CB )) or resid 361 through 363 or (resid 3 \ 64 through 373 and (name N or name CA or name C or name O or name CB )) or resid \ 374 through 375 or (resid 376 through 378 and (name N or name CA or name C or n \ ame O or name CB )) or resid 379 or (resid 380 and (name N or name CA or name C \ or name O or name CB )) or resid 381 or (resid 382 through 383 and (name N or na \ me CA or name C or name O or name CB )) or resid 384 or (resid 385 through 390 a \ nd (name N or name CA or name C or name O or name CB )) or resid 391 through 397 \ or (resid 398 through 403 and (name N or name CA or name C or name O or name CB \ )) or (resid 404 through 411 and (name N or name CA or name C or name O or name \ CB )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA \ or name C or name O or name CB )) or resid 416 or (resid 417 through 425 and (n \ ame N or name CA or name C or name O or name CB )) or resid 426 through 428 or ( \ resid 429 through 430 and (name N or name CA or name C or name O or name CB )) o \ r resid 431 through 432 or (resid 433 through 437 and (name N or name CA or name \ C or name O or name CB )) or resid 438 through 441 or (resid 442 through 445 an \ d (name N or name CA or name C or name O or name CB )) or resid 446 through 447 \ or (resid 448 through 462 and (name N or name CA or name C or name O or name CB \ )) or resid 463 or (resid 464 through 475 and (name N or name CA or name C or na \ me O or name CB )) or resid 476 through 488 or (resid 489 through 490 and (name \ N or name CA or name C or name O or name CB )) or resid 491 or (resid 492 throug \ h 495 and (name N or name CA or name C or name O or name CB )) or resid 496 or ( \ resid 497 through 498 and (name N or name CA or name C or name O or name CB )) o \ r resid 499 through 500 or (resid 501 and (name N or name CA or name C or name O \ or name CB )) or resid 502 through 504 or (resid 505 and (name N or name CA or \ name C or name O or name CB )) or resid 506 through 507 or (resid 508 through 52 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 521 through \ 522 or (resid 523 through 524 and (name N or name CA or name C or name O or name \ CB )) or resid 525 through 527 or (resid 528 through 531 and (name N or name CA \ or name C or name O or name CB )) or resid 532 through 536 or (resid 537 and (n \ ame N or name CA or name C or name O or name CB )) or resid 538 through 553 or ( \ resid 554 and (name N or name CA or name C or name O or name CB )) or resid 555 \ through 580 or (resid 581 and (name N or name CA or name C or name O or name CB \ )) or resid 582 or (resid 583 and (name N or name CA or name C or name O or name \ CB )) or resid 584 through 653 or (resid 654 and (name N or name CA or name C o \ r name O or name CB )) or resid 655 through 675 or (resid 676 and (name N or nam \ e CA or name C or name O or name CB )) or resid 690 through 701 or (resid 702 an \ d (name N or name CA or name C or name O or name CB )) or resid 703 through 744 \ or (resid 745 through 746 and (name N or name CA or name C or name O or name CB \ )) or resid 747 or (resid 748 and (name N or name CA or name C or name O or name \ CB )) or resid 749 or (resid 750 and (name N or name CA or name C or name O or \ name CB )) or resid 751 through 757 or (resid 758 and (name N or name CA or name \ C or name O or name CB )) or resid 759 through 785 or (resid 786 and (name N or \ name CA or name C or name O or name CB )) or resid 787 through 793 or (resid 79 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 795 through \ 810 or (resid 811 and (name N or name CA or name C or name O or name CB )) or re \ sid 812 through 813 or (resid 814 and (name N or name CA or name C or name O or \ name CB )) or resid 815 through 936 or (resid 937 and (name N or name CA or name \ C or name O or name CB )) or resid 938 or (resid 939 through 941 and (name N or \ name CA or name C or name O or name CB )) or resid 942 through 973 or (resid 97 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 975 through \ 987 or (resid 988 through 989 and (name N or name CA or name C or name O or name \ CB )) or resid 990 through 1091 or (resid 1092 and (name N or name CA or name C \ or name O or name CB )) or resid 1093 through 1126 or (resid 1127 and (name N o \ r name CA or name C or name O or name CB )) or resid 1128 through 1141 or (resid \ 1142 and (name N or name CA or name C or name O or name CB )) or resid 1143 thr \ ough 1146 or (resid 1147 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1304 through 1309)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 86 or (resid 87 and (nam \ e N or name CA or name C or name O or name CB )) or resid 88 through 93 or (resi \ d 94 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 through 107 or (resid 108 through 110 and (name N or name CA or name C or \ name O or name CB )) or (resid 116 and (name N or name CA or name C or name O o \ r name CB )) or resid 117 through 119 or (resid 120 and (name N or name CA or na \ me C or name O or name CB )) or resid 121 through 125 or (resid 126 through 129 \ and (name N or name CA or name C or name O or name CB )) or resid 130 through 13 \ 3 or (resid 134 and (name N or name CA or name C or name O or name CB )) or resi \ d 135 or (resid 138 and (name N or name CA or name C or name O or name CB )) or \ resid 139 or (resid 140 and (name N or name CA or name C or name O or name CB )) \ or resid 166 or (resid 167 through 190 and (name N or name CA or name C or name \ O or name CB )) or resid 191 through 197 or (resid 198 and (name N or name CA o \ r name C or name O or name CB )) or resid 199 through 204 or (resid 205 and (nam \ e N or name CA or name C or name O or name CB )) or resid 206 through 207 or (re \ sid 208 and (name N or name CA or name C or name O or name CB )) or resid 209 th \ rough 217 or (resid 218 and (name N or name CA or name C or name O or name CB )) \ or resid 219 through 228 or (resid 229 and (name N or name CA or name C or name \ O or name CB )) or resid 230 through 280 or (resid 281 and (name N or name CA o \ r name C or name O or name CB )) or resid 282 through 323 or (resid 324 and (nam \ e N or name CA or name C or name O or name CB )) or resid 325 through 331 or (re \ sid 332 through 335 and (name N or name CA or name C or name O or name CB )) or \ resid 336 through 339 or (resid 340 through 342 and (name N or name CA or name C \ or name O or name CB )) or resid 343 through 344 or (resid 345 through 346 and \ (name N or name CA or name C or name O or name CB )) or resid 347 through 348 or \ (resid 349 through 352 and (name N or name CA or name C or name O or name CB )) \ or resid 353 through 356 or (resid 357 and (name N or name CA or name C or name \ O or name CB )) or resid 358 or (resid 359 through 360 and (name N or name CA o \ r name C or name O or name CB )) or resid 361 through 363 or (resid 364 through \ 373 and (name N or name CA or name C or name O or name CB )) or resid 374 or (re \ sid 375 through 378 and (name N or name CA or name C or name O or name CB )) or \ resid 379 or (resid 380 and (name N or name CA or name C or name O or name CB )) \ or resid 381 or (resid 382 through 383 and (name N or name CA or name C or name \ O or name CB )) or resid 384 or (resid 385 through 390 and (name N or name CA o \ r name C or name O or name CB )) or resid 391 through 393 or (resid 394 and (nam \ e N or name CA or name C or name O or name CB )) or resid 395 through 397 or (re \ sid 398 through 403 and (name N or name CA or name C or name O or name CB )) or \ resid 404 or (resid 405 through 411 and (name N or name CA or name C or name O o \ r name CB )) or resid 412 through 413 or (resid 414 through 415 and (name N or n \ ame CA or name C or name O or name CB )) or resid 416 or (resid 417 through 425 \ and (name N or name CA or name C or name O or name CB )) or resid 426 or (resid \ 427 through 430 and (name N or name CA or name C or name O or name CB )) or resi \ d 431 through 432 or (resid 433 through 437 and (name N or name CA or name C or \ name O or name CB )) or resid 438 through 440 or (resid 441 through 445 and (nam \ e N or name CA or name C or name O or name CB )) or resid 446 through 447 or (re \ sid 448 through 462 and (name N or name CA or name C or name O or name CB )) or \ resid 463 or (resid 464 through 475 and (name N or name CA or name C or name O o \ r name CB )) or resid 476 or (resid 477 through 478 and (name N or name CA or na \ me C or name O or name CB )) or resid 479 through 480 or (resid 481 and (name N \ or name CA or name C or name O or name CB )) or resid 482 or (resid 483 through \ 484 and (name N or name CA or name C or name O or name CB )) or resid 485 or (re \ sid 486 through 487 and (name N or name CA or name C or name O or name CB )) or \ resid 488 or (resid 489 through 490 and (name N or name CA or name C or name O o \ r name CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or na \ me C or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N \ or name CA or name C or name O or name CB )) or resid 499 or (resid 500 through \ 501 and (name N or name CA or name C or name O or name CB )) or resid 502 throug \ h 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) or \ resid 506 through 507 or (resid 508 through 520 and (name N or name CA or name C \ or name O or name CB )) or resid 521 through 522 or (resid 523 through 524 and \ (name N or name CA or name C or name O or name CB )) or resid 525 through 527 or \ (resid 528 through 531 and (name N or name CA or name C or name O or name CB )) \ or resid 532 through 536 or (resid 537 and (name N or name CA or name C or name \ O or name CB )) or resid 538 through 555 or (resid 556 and (name N or name CA o \ r name C or name O or name CB )) or resid 557 or (resid 558 and (name N or name \ CA or name C or name O or name CB )) or resid 559 through 580 or (resid 581 and \ (name N or name CA or name C or name O or name CB )) or resid 582 through 621 or \ resid 628 through 631 or (resid 632 and (name N or name CA or name C or name O \ or name CB )) or resid 633 through 645 or (resid 646 through 647 and (name N or \ name CA or name C or name O or name CB )) or resid 648 through 653 or (resid 654 \ and (name N or name CA or name C or name O or name CB )) or resid 655 through 7 \ 44 or (resid 745 through 746 and (name N or name CA or name C or name O or name \ CB )) or resid 747 or (resid 748 and (name N or name CA or name C or name O or n \ ame CB )) or resid 749 or (resid 750 and (name N or name CA or name C or name O \ or name CB )) or resid 751 through 757 or (resid 758 and (name N or name CA or n \ ame C or name O or name CB )) or resid 759 through 809 or (resid 810 through 811 \ and (name N or name CA or name C or name O or name CB )) or resid 812 through 8 \ 13 or (resid 814 and (name N or name CA or name C or name O or name CB )) or res \ id 815 through 827 or resid 856 through 936 or (resid 937 and (name N or name CA \ or name C or name O or name CB )) or resid 938 or (resid 939 through 941 and (n \ ame N or name CA or name C or name O or name CB )) or resid 942 through 973 or ( \ resid 974 and (name N or name CA or name C or name O or name CB )) or resid 975 \ through 984 or (resid 985 and (name N or name CA or name C or name O or name CB \ )) or resid 986 through 987 or (resid 988 through 989 and (name N or name CA or \ name C or name O or name CB )) or resid 990 through 1126 or (resid 1127 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1128 through 1141 or ( \ resid 1142 and (name N or name CA or name C or name O or name CB )) or resid 114 \ 3 through 1147 or resid 1302 through 1307)) selection = (chain 'C' and (resid 27 through 110 or resid 116 through 126 or (resid 127 thro \ ugh 129 and (name N or name CA or name C or name O or name CB )) or resid 130 th \ rough 135 or resid 138 through 140 or resid 166 through 172 or (resid 187 throug \ h 190 and (name N or name CA or name C or name O or name CB )) or resid 191 thro \ ugh 220 or (resid 221 through 222 and (name N or name CA or name C or name O or \ name CB )) or resid 223 through 227 or (resid 228 through 229 and (name N or nam \ e CA or name C or name O or name CB )) or resid 230 through 236 or (resid 237 an \ d (name N or name CA or name C or name O or name CB )) or resid 238 through 393 \ or (resid 394 and (name N or name CA or name C or name O or name CB )) or resid \ 395 through 440 or (resid 441 through 445 and (name N or name CA or name C or na \ me O or name CB )) or resid 446 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 or (resid 556 and (name N or nam \ e CA or name C or name O or name CB )) or resid 557 or (resid 558 and (name N or \ name CA or name C or name O or name CB )) or resid 559 through 567 or (resid 56 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 569 through \ 621 or resid 628 through 631 or (resid 632 and (name N or name CA or name C or n \ ame O or name CB )) or resid 633 through 645 or (resid 646 through 647 and (name \ N or name CA or name C or name O or name CB )) or resid 648 through 675 or (res \ id 676 and (name N or name CA or name C or name O or name CB )) or resid 690 thr \ ough 701 or (resid 702 and (name N or name CA or name C or name O or name CB )) \ or resid 703 through 793 or (resid 794 and (name N or name CA or name C or name \ O or name CB )) or resid 795 through 809 or (resid 810 through 811 and (name N o \ r name CA or name C or name O or name CB )) or resid 812 or (resid 813 through 8 \ 14 and (name N or name CA or name C or name O or name CB )) or resid 815 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or r \ esid 986 through 1146 or (resid 1147 and (name N or name CA or name C or name O \ or name CB )) or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'O' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.940 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:10.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 : 0.010 0.076 26898 Z= 0.427 Angle : 0.849 19.860 36821 Z= 0.443 Chirality : 0.057 1.285 4399 Planarity : 0.005 0.056 4668 Dihedral : 14.994 112.278 10320 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.11 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.58 (0.14), residues: 3331 helix: 0.68 (0.20), residues: 693 sheet: -0.68 (0.18), residues: 767 loop : -1.96 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 214 TYR 0.026 0.002 TYR A 266 PHE 0.047 0.002 PHE C 906 TRP 0.033 0.003 TRP C 886 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.01007 (26790) covalent geometry : angle 0.81751 (36542) SS BOND : bond 0.00485 ( 45) SS BOND : angle 1.56567 ( 90) hydrogen bonds : bond 0.14189 ( 1037) hydrogen bonds : angle 6.89031 ( 2874) link_BETA1-4 : bond 0.00613 ( 23) link_BETA1-4 : angle 2.39092 ( 69) link_NAG-ASN : bond 0.00617 ( 40) link_NAG-ASN : angle 3.53758 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8864 (m-10) cc_final: 0.8580 (m-10) REVERT: C 265 TYR cc_start: 0.7258 (m-10) cc_final: 0.6966 (m-10) REVERT: B 628 GLN cc_start: 0.9048 (mm110) cc_final: 0.8800 (mm110) REVERT: E 93 LYS cc_start: 0.8109 (tmmt) cc_final: 0.7809 (tmmm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.5943 time to fit residues: 66.9136 Evaluate side-chains 75 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.0030 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN C1106 GLN H 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.105841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.061410 restraints weight = 69545.181| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 4.37 r_work: 0.2652 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26898 Z= 0.131 Angle : 0.633 17.752 36821 Z= 0.317 Chirality : 0.048 0.835 4399 Planarity : 0.005 0.051 4668 Dihedral : 9.767 69.483 4904 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 0.34 % Allowed : 4.42 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.01 (0.14), residues: 3331 helix: 1.48 (0.21), residues: 678 sheet: -0.28 (0.19), residues: 724 loop : -1.70 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 403 TYR 0.017 0.001 TYR A1067 PHE 0.017 0.001 PHE B 400 TRP 0.014 0.001 TRP D 36 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00290 (26790) covalent geometry : angle 0.60496 (36542) SS BOND : bond 0.00331 ( 45) SS BOND : angle 1.15594 ( 90) hydrogen bonds : bond 0.05218 ( 1037) hydrogen bonds : angle 5.58066 ( 2874) link_BETA1-4 : bond 0.00538 ( 23) link_BETA1-4 : angle 2.21689 ( 69) link_NAG-ASN : bond 0.00377 ( 40) link_NAG-ASN : angle 2.77861 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.780 Fit side-chains REVERT: C 237 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7943 (mmm-85) REVERT: B 628 GLN cc_start: 0.9115 (mm110) cc_final: 0.8787 (mm110) REVERT: H 82 MET cc_start: 0.3896 (ppp) cc_final: 0.3456 (pmm) REVERT: E 102 TYR cc_start: 0.7777 (t80) cc_final: 0.7541 (t80) REVERT: E 103 TRP cc_start: 0.7308 (m-90) cc_final: 0.6750 (m-90) REVERT: D 102 TYR cc_start: 0.6272 (t80) cc_final: 0.5991 (t80) outliers start: 9 outliers final: 2 residues processed: 90 average time/residue: 0.5671 time to fit residues: 61.3023 Evaluate side-chains 80 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 286 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 133 optimal weight: 30.0000 chunk 94 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 273 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.104581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.059391 restraints weight = 70277.925| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.83 r_work: 0.2663 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26898 Z= 0.150 Angle : 0.600 17.004 36821 Z= 0.297 Chirality : 0.047 0.793 4399 Planarity : 0.004 0.052 4668 Dihedral : 7.611 56.797 4904 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 0.64 % Allowed : 6.95 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.72 (0.14), residues: 3331 helix: 1.75 (0.21), residues: 680 sheet: -0.03 (0.18), residues: 756 loop : -1.58 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 403 TYR 0.020 0.001 TYR E 37 PHE 0.016 0.001 PHE C 906 TRP 0.011 0.001 TRP C 886 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00351 (26790) covalent geometry : angle 0.57272 (36542) SS BOND : bond 0.00345 ( 45) SS BOND : angle 1.06821 ( 90) hydrogen bonds : bond 0.05073 ( 1037) hydrogen bonds : angle 5.22438 ( 2874) link_BETA1-4 : bond 0.00561 ( 23) link_BETA1-4 : angle 2.08233 ( 69) link_NAG-ASN : bond 0.00346 ( 40) link_NAG-ASN : angle 2.70792 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 237 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7787 (mmm-85) REVERT: C 265 TYR cc_start: 0.7399 (m-10) cc_final: 0.6985 (m-10) REVERT: B 628 GLN cc_start: 0.9091 (mm110) cc_final: 0.8649 (mm-40) REVERT: E 37 TYR cc_start: 0.7321 (m-10) cc_final: 0.7121 (m-10) REVERT: D 102 TYR cc_start: 0.5993 (t80) cc_final: 0.5602 (t80) outliers start: 17 outliers final: 6 residues processed: 89 average time/residue: 0.5601 time to fit residues: 60.0568 Evaluate side-chains 82 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 912 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 49 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 135 optimal weight: 50.0000 chunk 42 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS B 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.103340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.058127 restraints weight = 70076.242| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.81 r_work: 0.2620 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 26898 Z= 0.286 Angle : 0.668 18.669 36821 Z= 0.333 Chirality : 0.049 0.882 4399 Planarity : 0.004 0.046 4668 Dihedral : 7.301 59.944 4904 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 1.02 % Allowed : 8.58 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.79 (0.14), residues: 3331 helix: 1.61 (0.21), residues: 680 sheet: -0.10 (0.18), residues: 773 loop : -1.60 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.019 0.001 TYR C 266 PHE 0.017 0.002 PHE C 906 TRP 0.013 0.002 TRP C 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00692 (26790) covalent geometry : angle 0.64079 (36542) SS BOND : bond 0.00393 ( 45) SS BOND : angle 1.18926 ( 90) hydrogen bonds : bond 0.05981 ( 1037) hydrogen bonds : angle 5.35491 ( 2874) link_BETA1-4 : bond 0.00494 ( 23) link_BETA1-4 : angle 2.01221 ( 69) link_NAG-ASN : bond 0.00429 ( 40) link_NAG-ASN : angle 2.91038 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.993 Fit side-chains REVERT: C 237 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7513 (mtp-110) REVERT: C 265 TYR cc_start: 0.7460 (m-10) cc_final: 0.7027 (m-10) REVERT: B 628 GLN cc_start: 0.9085 (mm110) cc_final: 0.8634 (mm-40) REVERT: E 37 TYR cc_start: 0.7420 (m-10) cc_final: 0.6997 (m-10) REVERT: E 102 TYR cc_start: 0.8266 (t80) cc_final: 0.8014 (t80) REVERT: E 103 TRP cc_start: 0.7706 (m-90) cc_final: 0.7494 (m-90) REVERT: D 22 CYS cc_start: 0.3989 (t) cc_final: 0.3691 (p) REVERT: D 102 TYR cc_start: 0.5931 (t80) cc_final: 0.5539 (t80) outliers start: 27 outliers final: 7 residues processed: 96 average time/residue: 0.4749 time to fit residues: 56.4677 Evaluate side-chains 81 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 290 optimal weight: 0.3980 chunk 209 optimal weight: 4.9990 chunk 273 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 298 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.105093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.060035 restraints weight = 69650.353| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.83 r_work: 0.2666 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26898 Z= 0.136 Angle : 0.578 16.657 36821 Z= 0.287 Chirality : 0.046 0.793 4399 Planarity : 0.004 0.046 4668 Dihedral : 6.769 56.523 4904 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 0.83 % Allowed : 9.56 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.57 (0.14), residues: 3331 helix: 1.79 (0.21), residues: 681 sheet: 0.07 (0.18), residues: 758 loop : -1.45 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 TYR 0.018 0.001 TYR B 365 PHE 0.014 0.001 PHE A 400 TRP 0.010 0.001 TRP D 36 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00318 (26790) covalent geometry : angle 0.55149 (36542) SS BOND : bond 0.00349 ( 45) SS BOND : angle 1.07270 ( 90) hydrogen bonds : bond 0.04797 ( 1037) hydrogen bonds : angle 5.08593 ( 2874) link_BETA1-4 : bond 0.00552 ( 23) link_BETA1-4 : angle 1.86161 ( 69) link_NAG-ASN : bond 0.00326 ( 40) link_NAG-ASN : angle 2.63276 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.975 Fit side-chains REVERT: C 237 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7797 (mmm-85) REVERT: C 265 TYR cc_start: 0.7352 (m-10) cc_final: 0.6929 (m-10) REVERT: B 628 GLN cc_start: 0.9056 (mm110) cc_final: 0.8728 (mm110) REVERT: E 37 TYR cc_start: 0.7501 (m-10) cc_final: 0.7112 (m-10) REVERT: E 102 TYR cc_start: 0.8425 (t80) cc_final: 0.8128 (t80) REVERT: E 103 TRP cc_start: 0.7788 (OUTLIER) cc_final: 0.7563 (m-90) REVERT: D 102 TYR cc_start: 0.5958 (t80) cc_final: 0.5545 (t80) outliers start: 22 outliers final: 10 residues processed: 93 average time/residue: 0.4704 time to fit residues: 54.6674 Evaluate side-chains 89 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 103 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 261 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 189 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 288 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 258 optimal weight: 0.0060 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.104404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.059411 restraints weight = 69878.048| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.81 r_work: 0.2641 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26898 Z= 0.168 Angle : 0.586 16.866 36821 Z= 0.291 Chirality : 0.046 0.798 4399 Planarity : 0.004 0.048 4668 Dihedral : 6.625 57.038 4904 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 1.13 % Allowed : 10.65 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.50 (0.14), residues: 3331 helix: 1.84 (0.21), residues: 681 sheet: 0.12 (0.18), residues: 755 loop : -1.41 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 TYR 0.017 0.001 TYR A1067 PHE 0.015 0.001 PHE C 392 TRP 0.009 0.001 TRP E 103 HIS 0.005 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00404 (26790) covalent geometry : angle 0.56002 (36542) SS BOND : bond 0.00329 ( 45) SS BOND : angle 1.09713 ( 90) hydrogen bonds : bond 0.04997 ( 1037) hydrogen bonds : angle 5.04148 ( 2874) link_BETA1-4 : bond 0.00516 ( 23) link_BETA1-4 : angle 1.80643 ( 69) link_NAG-ASN : bond 0.00332 ( 40) link_NAG-ASN : angle 2.66234 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.991 Fit side-chains REVERT: C 237 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7776 (mmm-85) REVERT: B 628 GLN cc_start: 0.9042 (mm110) cc_final: 0.8584 (mm-40) REVERT: E 37 TYR cc_start: 0.7502 (m-10) cc_final: 0.7064 (m-10) REVERT: E 102 TYR cc_start: 0.8498 (t80) cc_final: 0.8238 (t80) REVERT: E 103 TRP cc_start: 0.7814 (m-90) cc_final: 0.7504 (m-90) REVERT: D 4 LEU cc_start: 0.2752 (OUTLIER) cc_final: 0.0903 (tm) REVERT: D 102 TYR cc_start: 0.5915 (t80) cc_final: 0.5547 (t80) outliers start: 30 outliers final: 13 residues processed: 104 average time/residue: 0.4758 time to fit residues: 61.1783 Evaluate side-chains 90 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain D residue 4 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 51 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 227 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 138 optimal weight: 50.0000 chunk 333 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.103681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.058641 restraints weight = 70024.173| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.77 r_work: 0.2625 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26898 Z= 0.208 Angle : 0.607 17.384 36821 Z= 0.302 Chirality : 0.047 0.823 4399 Planarity : 0.004 0.047 4668 Dihedral : 6.589 57.875 4904 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 1.06 % Allowed : 11.56 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.52 (0.14), residues: 3331 helix: 1.82 (0.21), residues: 680 sheet: 0.11 (0.18), residues: 760 loop : -1.42 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.018 0.001 TYR B 365 PHE 0.015 0.001 PHE C 392 TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00502 (26790) covalent geometry : angle 0.58125 (36542) SS BOND : bond 0.00329 ( 45) SS BOND : angle 1.10832 ( 90) hydrogen bonds : bond 0.05338 ( 1037) hydrogen bonds : angle 5.09076 ( 2874) link_BETA1-4 : bond 0.00507 ( 23) link_BETA1-4 : angle 1.79724 ( 69) link_NAG-ASN : bond 0.00350 ( 40) link_NAG-ASN : angle 2.73829 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 1.048 Fit side-chains REVERT: C 237 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7828 (mmm-85) REVERT: C 265 TYR cc_start: 0.7443 (m-10) cc_final: 0.7173 (m-10) REVERT: B 628 GLN cc_start: 0.9028 (mm110) cc_final: 0.8575 (mm-40) REVERT: E 37 TYR cc_start: 0.7505 (m-10) cc_final: 0.6979 (m-10) REVERT: E 102 TYR cc_start: 0.8586 (t80) cc_final: 0.8358 (t80) REVERT: E 103 TRP cc_start: 0.7861 (m-90) cc_final: 0.7470 (m-90) REVERT: D 102 TYR cc_start: 0.5875 (t80) cc_final: 0.5530 (t80) outliers start: 28 outliers final: 13 residues processed: 100 average time/residue: 0.4659 time to fit residues: 57.7628 Evaluate side-chains 89 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 138 optimal weight: 50.0000 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 238 optimal weight: 20.0000 chunk 305 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 272 optimal weight: 0.6980 chunk 70 optimal weight: 0.0870 chunk 175 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 606 ASN B 474 GLN B 481 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.104316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.059838 restraints weight = 70377.902| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.70 r_work: 0.2685 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26898 Z= 0.111 Angle : 0.560 15.909 36821 Z= 0.277 Chirality : 0.045 0.750 4399 Planarity : 0.004 0.047 4668 Dihedral : 6.261 56.751 4904 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 0.72 % Allowed : 12.16 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.35 (0.15), residues: 3331 helix: 2.00 (0.21), residues: 681 sheet: 0.21 (0.18), residues: 761 loop : -1.32 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.017 0.001 TYR A1067 PHE 0.018 0.001 PHE B 565 TRP 0.010 0.001 TRP D 36 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00250 (26790) covalent geometry : angle 0.53615 (36542) SS BOND : bond 0.00292 ( 45) SS BOND : angle 0.93748 ( 90) hydrogen bonds : bond 0.04409 ( 1037) hydrogen bonds : angle 4.88570 ( 2874) link_BETA1-4 : bond 0.00557 ( 23) link_BETA1-4 : angle 1.74210 ( 69) link_NAG-ASN : bond 0.00330 ( 40) link_NAG-ASN : angle 2.53121 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: C 237 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7871 (mmm-85) REVERT: C 265 TYR cc_start: 0.7395 (m-10) cc_final: 0.7181 (m-10) REVERT: B 628 GLN cc_start: 0.9044 (mm110) cc_final: 0.8611 (mm-40) REVERT: E 37 TYR cc_start: 0.7454 (m-10) cc_final: 0.7004 (m-10) REVERT: E 102 TYR cc_start: 0.8644 (t80) cc_final: 0.8434 (t80) REVERT: D 4 LEU cc_start: 0.3340 (OUTLIER) cc_final: 0.1388 (tp) REVERT: D 102 TYR cc_start: 0.5707 (t80) cc_final: 0.5340 (t80) outliers start: 19 outliers final: 12 residues processed: 96 average time/residue: 0.4932 time to fit residues: 57.9531 Evaluate side-chains 89 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain D residue 4 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 125 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 99 optimal weight: 0.0870 chunk 81 optimal weight: 0.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 625 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.105199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.060608 restraints weight = 69911.428| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.76 r_work: 0.2688 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26898 Z= 0.107 Angle : 0.549 15.414 36821 Z= 0.271 Chirality : 0.045 0.715 4399 Planarity : 0.004 0.050 4668 Dihedral : 6.024 56.460 4904 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 0.57 % Allowed : 12.50 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.17 (0.15), residues: 3331 helix: 2.18 (0.21), residues: 691 sheet: 0.32 (0.18), residues: 777 loop : -1.26 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 983 TYR 0.023 0.001 TYR B 365 PHE 0.017 0.001 PHE C 392 TRP 0.010 0.001 TRP D 36 HIS 0.005 0.000 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00242 (26790) covalent geometry : angle 0.52580 (36542) SS BOND : bond 0.00275 ( 45) SS BOND : angle 0.86826 ( 90) hydrogen bonds : bond 0.04119 ( 1037) hydrogen bonds : angle 4.74136 ( 2874) link_BETA1-4 : bond 0.00564 ( 23) link_BETA1-4 : angle 1.70074 ( 69) link_NAG-ASN : bond 0.00328 ( 40) link_NAG-ASN : angle 2.46516 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.968 Fit side-chains REVERT: C 237 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7639 (mtp85) REVERT: C 265 TYR cc_start: 0.7378 (m-10) cc_final: 0.7155 (m-10) REVERT: B 586 ASP cc_start: 0.8034 (m-30) cc_final: 0.7819 (m-30) REVERT: B 628 GLN cc_start: 0.9022 (mm110) cc_final: 0.8583 (mm-40) REVERT: E 2 VAL cc_start: 0.7737 (p) cc_final: 0.7084 (p) REVERT: E 37 TYR cc_start: 0.7528 (m-10) cc_final: 0.7027 (m-10) REVERT: E 101 ASP cc_start: 0.8777 (p0) cc_final: 0.8564 (p0) REVERT: E 102 TYR cc_start: 0.8627 (t80) cc_final: 0.8334 (t80) REVERT: E 103 TRP cc_start: 0.7860 (m-90) cc_final: 0.7429 (m-90) REVERT: D 4 LEU cc_start: 0.2422 (OUTLIER) cc_final: 0.0638 (tm) REVERT: D 102 TYR cc_start: 0.5987 (t80) cc_final: 0.5619 (t80) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.4693 time to fit residues: 53.9289 Evaluate side-chains 88 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain D residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 37 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 189 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 HIS H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.103047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.057933 restraints weight = 70341.804| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.80 r_work: 0.2612 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 26898 Z= 0.342 Angle : 0.696 18.638 36821 Z= 0.346 Chirality : 0.050 0.886 4399 Planarity : 0.004 0.051 4668 Dihedral : 6.516 59.126 4904 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.66 % Rotamer: Outliers : 0.79 % Allowed : 12.50 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.50 (0.14), residues: 3331 helix: 1.82 (0.21), residues: 682 sheet: 0.14 (0.18), residues: 780 loop : -1.42 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 983 TYR 0.017 0.002 TYR A1067 PHE 0.020 0.002 PHE C1121 TRP 0.010 0.002 TRP C 886 HIS 0.005 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00831 (26790) covalent geometry : angle 0.67068 (36542) SS BOND : bond 0.00376 ( 45) SS BOND : angle 1.22867 ( 90) hydrogen bonds : bond 0.06194 ( 1037) hydrogen bonds : angle 5.22050 ( 2874) link_BETA1-4 : bond 0.00475 ( 23) link_BETA1-4 : angle 1.83112 ( 69) link_NAG-ASN : bond 0.00476 ( 40) link_NAG-ASN : angle 2.90767 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: C 265 TYR cc_start: 0.7503 (m-10) cc_final: 0.7259 (m-10) REVERT: B 628 GLN cc_start: 0.9035 (mm110) cc_final: 0.8594 (mm-40) REVERT: E 2 VAL cc_start: 0.7877 (p) cc_final: 0.7435 (p) REVERT: E 37 TYR cc_start: 0.7565 (m-10) cc_final: 0.7034 (m-10) REVERT: E 102 TYR cc_start: 0.8693 (t80) cc_final: 0.8446 (t80) REVERT: E 103 TRP cc_start: 0.7722 (m-90) cc_final: 0.7248 (m-90) REVERT: D 4 LEU cc_start: 0.3559 (OUTLIER) cc_final: 0.1496 (tt) REVERT: D 102 TYR cc_start: 0.5845 (t80) cc_final: 0.5442 (t80) outliers start: 21 outliers final: 13 residues processed: 97 average time/residue: 0.4532 time to fit residues: 54.9314 Evaluate side-chains 91 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain D residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 145 optimal weight: 3.9990 chunk 271 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 149 optimal weight: 0.3980 chunk 202 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 273 optimal weight: 0.8980 chunk 234 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.104593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.059821 restraints weight = 69587.105| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.73 r_work: 0.2669 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26898 Z= 0.113 Angle : 0.569 15.932 36821 Z= 0.280 Chirality : 0.045 0.753 4399 Planarity : 0.004 0.047 4668 Dihedral : 6.126 58.059 4904 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 0.60 % Allowed : 12.88 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.24 (0.15), residues: 3331 helix: 2.13 (0.21), residues: 667 sheet: 0.31 (0.18), residues: 763 loop : -1.27 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.028 0.001 TYR B 365 PHE 0.016 0.001 PHE C 392 TRP 0.011 0.001 TRP D 36 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00255 (26790) covalent geometry : angle 0.54583 (36542) SS BOND : bond 0.00292 ( 45) SS BOND : angle 0.91541 ( 90) hydrogen bonds : bond 0.04421 ( 1037) hydrogen bonds : angle 4.87172 ( 2874) link_BETA1-4 : bond 0.00526 ( 23) link_BETA1-4 : angle 1.72246 ( 69) link_NAG-ASN : bond 0.00352 ( 40) link_NAG-ASN : angle 2.51469 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8957.11 seconds wall clock time: 153 minutes 17.15 seconds (9197.15 seconds total)