Starting phenix.real_space_refine on Mon Aug 25 18:49:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8heb_34686/08_2025/8heb_34686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8heb_34686/08_2025/8heb_34686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8heb_34686/08_2025/8heb_34686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8heb_34686/08_2025/8heb_34686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8heb_34686/08_2025/8heb_34686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8heb_34686/08_2025/8heb_34686.map" } resolution = 3.53 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= 0.041 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 141 5.16 5 C 18981 2.51 5 N 4895 2.21 5 O 5895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29912 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7980 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 51, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'PHE:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 7982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7982 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 51, 'TRANS': 976} Chain breaks: 7 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 7974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7974 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 51, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 1, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "G" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "H" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "Y" 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: "Z" 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: 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: "B" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.99, per 1000 atoms: 0.27 Number of scatterers: 29912 At special positions: 0 Unit cell: (154.98, 147.6, 217.3, 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 141 16.00 O 5895 8.00 N 4895 7.00 C 18981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 87 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6998 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 69 sheets defined 21.8% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.593A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.768A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.511A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.982A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.590A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 738 through 743 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 761 through 783 removed outlier: 3.655A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.532A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.107A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.588A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.895A 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 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.236A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.537A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.593A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.088A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 761 through 783 removed outlier: 3.773A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.068A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.284A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.685A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.512A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1033 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.911A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.627A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.787A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.149A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 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 758 through 783 removed outlier: 4.155A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.081A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.710A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.191A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.968A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.382A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.794A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.937A pdb=" N ALA D 82 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.939A pdb=" N ALA F 82 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'H' and resid 78 through 82 removed outlier: 3.914A pdb=" N ALA H 82 " --> pdb=" O CYS H 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 31 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.808A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.575A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.524A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.444A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.859A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.709A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.386A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.091A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.720A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 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 1125 removed outlier: 4.416A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.619A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.060A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.172A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 132 through 135 removed outlier: 6.717A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.146A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.432A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.272A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.875A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.621A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.541A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.084A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.909A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.345A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.447A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.882A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 553 through 554 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.144A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.975A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.586A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.544A pdb=" N VAL D 18 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.598A pdb=" N VAL D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 12 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 110 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE D 47 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.598A pdb=" N VAL D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 12 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 110 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY D 89 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA D 100 " --> pdb=" O GLY D 89 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.972A pdb=" N LEU E 17 " --> pdb=" O MET E 79 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET E 79 " --> pdb=" O LEU E 17 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.534A pdb=" N SER E 34 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG E 37 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TRP E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.508A pdb=" N VAL F 18 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 9 through 13 removed outlier: 3.603A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS F 110 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AG8, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.898A pdb=" N LEU G 17 " --> pdb=" O MET G 79 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET G 79 " --> pdb=" O LEU G 17 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.880A pdb=" N MET G 33 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.502A pdb=" N VAL H 18 " --> pdb=" O MET H 74 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS H 69 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.592A pdb=" N VAL H 108 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 12 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS H 110 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE H 47 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLN H 36 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU H 45 " --> pdb=" O GLN H 36 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.592A pdb=" N VAL H 108 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 12 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS H 110 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY H 89 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA H 100 " --> pdb=" O GLY H 89 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.897A pdb=" N LEU I 17 " --> pdb=" O MET I 79 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET I 79 " --> pdb=" O LEU I 17 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.563A pdb=" N GLY I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG I 37 " --> pdb=" O TRP I 46 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TRP I 46 " --> pdb=" O ARG I 37 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.839A pdb=" N PHE I 106 " --> pdb=" O ARG I 94 " (cutoff:3.500A) 1107 hydrogen bonds defined for protein. 2994 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.81 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9524 1.35 - 1.47: 7957 1.47 - 1.60: 12905 1.60 - 1.72: 0 1.72 - 1.84: 177 Bond restraints: 30563 Sorted by residual: bond pdb=" N GLY D 96 " pdb=" CA GLY D 96 " ideal model delta sigma weight residual 1.446 1.475 -0.029 9.50e-03 1.11e+04 9.43e+00 bond pdb=" N CYS D 98 " pdb=" CA CYS D 98 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.23e+00 bond pdb=" N CYS H 98 " pdb=" CA CYS H 98 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.21e+00 bond pdb=" N SER H 92 " pdb=" CA SER H 92 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.09e+00 bond pdb=" N SER H 95 " pdb=" CA SER H 95 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.00e+00 ... (remaining 30558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 40574 1.61 - 3.22: 910 3.22 - 4.83: 94 4.83 - 6.44: 35 6.44 - 8.05: 5 Bond angle restraints: 41618 Sorted by residual: angle pdb=" N ILE H 28 " pdb=" CA ILE H 28 " pdb=" C ILE H 28 " ideal model delta sigma weight residual 113.10 108.16 4.94 9.70e-01 1.06e+00 2.59e+01 angle pdb=" N ILE D 28 " pdb=" CA ILE D 28 " pdb=" C ILE D 28 " ideal model delta sigma weight residual 113.10 108.34 4.76 9.70e-01 1.06e+00 2.41e+01 angle pdb=" N ILE F 28 " pdb=" CA ILE F 28 " pdb=" C ILE F 28 " ideal model delta sigma weight residual 113.10 108.45 4.65 9.70e-01 1.06e+00 2.30e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.53 109.51 4.02 9.80e-01 1.04e+00 1.68e+01 angle pdb=" C SER F 92 " pdb=" CA SER F 92 " pdb=" CB SER F 92 " ideal model delta sigma weight residual 116.63 112.19 4.44 1.16e+00 7.43e-01 1.47e+01 ... (remaining 41613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16905 17.99 - 35.98: 1580 35.98 - 53.98: 340 53.98 - 71.97: 52 71.97 - 89.96: 30 Dihedral angle restraints: 18907 sinusoidal: 8012 harmonic: 10895 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -174.22 88.22 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -169.32 83.32 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 174.03 -81.03 1 1.00e+01 1.00e-02 8.10e+01 ... (remaining 18904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 4927 0.134 - 0.269: 12 0.269 - 0.403: 4 0.403 - 0.538: 0 0.538 - 0.672: 1 Chirality restraints: 4944 Sorted by residual: chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4941 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 81 " -0.012 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C ASN B 81 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN B 81 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO B 82 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO A 986 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO B 561 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " 0.026 5.00e-02 4.00e+02 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 249 2.62 - 3.19: 25525 3.19 - 3.76: 43134 3.76 - 4.33: 57943 4.33 - 4.90: 98907 Nonbonded interactions: 225758 Sorted by model distance: nonbonded pdb=" OD1 ASP A 568 " pdb=" N ILE A 569 " model vdw 2.053 3.120 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.205 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.211 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.221 3.040 ... (remaining 225753 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 15 through 553 or (resid 554 and (name N or name CA or nam \ e C or name O or name CB )) or resid 555 or (resid 556 and (name N or name CA or \ name C or name O or name CB )) or resid 557 through 827 or (resid 854 through 8 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 856 through \ 1309)) selection = (chain 'B' and (resid 15 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 337 or (resid 338 and (name N or n \ ame CA or name C or name O or name CB )) or resid 339 through 555 or (resid 556 \ and (name N or name CA or name C or name O or name CB )) or resid 557 or (resid \ 558 through 559 and (name N or name CA or name C or name O or name CB )) or resi \ d 560 through 785 or (resid 786 and (name N or name CA or name C or name O or na \ me CB )) or resid 787 through 827 or (resid 854 through 855 and (name N or name \ CA or name C or name O or name CB )) or resid 856 through 903 or (resid 904 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2 or name CE1 or name CE2 or name CZ )) or resid 905 through 1309)) selection = (chain 'C' and (resid 15 through 341 or (resid 342 and (name N or name CA or nam \ e C or name O or name CB )) or resid 343 through 553 or (resid 554 and (name N o \ r name CA or name C or name O or name CB )) or resid 555 through 557 or (resid 5 \ 58 through 559 and (name N or name CA or name C or name O or name CB )) or resid \ 560 through 827 or resid 854 through 903 or (resid 904 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or \ name CE2 or name CZ )) or resid 905 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.830 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30669 Z= 0.179 Angle : 0.597 14.200 41893 Z= 0.302 Chirality : 0.045 0.672 4944 Planarity : 0.003 0.056 5287 Dihedral : 14.173 89.959 11780 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 0.03 % Allowed : 13.40 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.14), residues: 3709 helix: 2.34 (0.22), residues: 635 sheet: 0.01 (0.17), residues: 932 loop : -1.06 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.019 0.001 TYR C 369 PHE 0.024 0.001 PHE A 201 TRP 0.011 0.001 TRP A 104 HIS 0.002 0.000 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00357 (30563) covalent geometry : angle 0.57257 (41618) SS BOND : bond 0.00372 ( 43) SS BOND : angle 1.07756 ( 86) hydrogen bonds : bond 0.23448 ( 1076) hydrogen bonds : angle 8.22722 ( 2994) link_BETA1-4 : bond 0.00358 ( 18) link_BETA1-4 : angle 1.09669 ( 54) link_NAG-ASN : bond 0.00444 ( 45) link_NAG-ASN : angle 2.88015 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 ASN cc_start: 0.8616 (p0) cc_final: 0.7925 (p0) outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.2064 time to fit residues: 44.9639 Evaluate side-chains 126 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 751 ASN B 992 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS F 1 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.160243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.110176 restraints weight = 70233.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.109634 restraints weight = 42683.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.109086 restraints weight = 32650.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.109633 restraints weight = 30088.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.109887 restraints weight = 26748.099| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30669 Z= 0.128 Angle : 0.554 13.205 41893 Z= 0.283 Chirality : 0.045 0.470 4944 Planarity : 0.004 0.050 5287 Dihedral : 6.626 59.781 5353 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.79 % Rotamer: Outliers : 1.78 % Allowed : 13.46 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.14), residues: 3709 helix: 2.15 (0.21), residues: 674 sheet: 0.25 (0.17), residues: 944 loop : -1.04 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.022 0.001 TYR A1067 PHE 0.013 0.001 PHE C 238 TRP 0.021 0.001 TRP A 104 HIS 0.003 0.001 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00288 (30563) covalent geometry : angle 0.52998 (41618) SS BOND : bond 0.00418 ( 43) SS BOND : angle 1.13856 ( 86) hydrogen bonds : bond 0.04942 ( 1076) hydrogen bonds : angle 5.94328 ( 2994) link_BETA1-4 : bond 0.00514 ( 18) link_BETA1-4 : angle 0.97039 ( 54) link_NAG-ASN : bond 0.00460 ( 45) link_NAG-ASN : angle 2.70504 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 503 VAL cc_start: 0.7707 (OUTLIER) cc_final: 0.7402 (m) REVERT: B 117 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7944 (tt) REVERT: E 30 ARG cc_start: 0.8484 (tpp80) cc_final: 0.8036 (mmp80) REVERT: G 30 ARG cc_start: 0.8439 (tpp80) cc_final: 0.7979 (mmp80) REVERT: G 79 MET cc_start: -0.0437 (pmm) cc_final: -0.0757 (pmm) REVERT: I 30 ARG cc_start: 0.8483 (tpp80) cc_final: 0.8023 (mmp80) REVERT: I 105 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7002 (tm-30) outliers start: 57 outliers final: 28 residues processed: 189 average time/residue: 0.1722 time to fit residues: 54.3910 Evaluate side-chains 155 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 333 optimal weight: 30.0000 chunk 298 optimal weight: 4.9990 chunk 301 optimal weight: 4.9990 chunk 341 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 339 optimal weight: 30.0000 chunk 87 optimal weight: 3.9990 chunk 350 optimal weight: 0.9990 chunk 290 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN D 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.155404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.097050 restraints weight = 66307.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.100560 restraints weight = 39521.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.100137 restraints weight = 29490.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.100859 restraints weight = 24543.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.101183 restraints weight = 24038.549| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 30669 Z= 0.266 Angle : 0.652 14.880 41893 Z= 0.328 Chirality : 0.047 0.495 4944 Planarity : 0.004 0.065 5287 Dihedral : 6.379 59.954 5353 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.15 % Rotamer: Outliers : 2.81 % Allowed : 14.84 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.14), residues: 3709 helix: 1.84 (0.21), residues: 673 sheet: 0.11 (0.17), residues: 956 loop : -1.21 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.028 0.002 TYR B 170 PHE 0.018 0.002 PHE A 92 TRP 0.011 0.001 TRP A 104 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00642 (30563) covalent geometry : angle 0.62338 (41618) SS BOND : bond 0.00454 ( 43) SS BOND : angle 1.88171 ( 86) hydrogen bonds : bond 0.05661 ( 1076) hydrogen bonds : angle 5.65826 ( 2994) link_BETA1-4 : bond 0.00319 ( 18) link_BETA1-4 : angle 1.09492 ( 54) link_NAG-ASN : bond 0.00533 ( 45) link_NAG-ASN : angle 3.04852 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 125 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.9317 (mp) cc_final: 0.9059 (tt) REVERT: A 733 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8251 (ttpp) REVERT: B 117 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8205 (tt) REVERT: C 342 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7022 (t80) REVERT: C 759 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7910 (t80) REVERT: E 79 MET cc_start: -0.0191 (pmm) cc_final: -0.0465 (pmm) REVERT: G 79 MET cc_start: -0.0135 (pmm) cc_final: -0.0479 (pmm) REVERT: I 30 ARG cc_start: 0.8664 (tpp80) cc_final: 0.8211 (mmp80) REVERT: I 105 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7143 (tm-30) outliers start: 90 outliers final: 54 residues processed: 208 average time/residue: 0.1597 time to fit residues: 55.8725 Evaluate side-chains 175 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 207 optimal weight: 1.9990 chunk 343 optimal weight: 40.0000 chunk 363 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 357 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 268 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 252 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.157655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.111412 restraints weight = 64128.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.108166 restraints weight = 40143.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.108382 restraints weight = 39808.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.108280 restraints weight = 32082.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.108458 restraints weight = 27481.004| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 30669 Z= 0.129 Angle : 0.548 13.626 41893 Z= 0.277 Chirality : 0.044 0.446 4944 Planarity : 0.003 0.051 5287 Dihedral : 5.823 59.817 5353 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 2.09 % Allowed : 16.62 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.14), residues: 3709 helix: 2.03 (0.21), residues: 671 sheet: 0.17 (0.17), residues: 958 loop : -1.13 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.028 0.001 TYR E 102 PHE 0.013 0.001 PHE C 238 TRP 0.013 0.001 TRP A 104 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00301 (30563) covalent geometry : angle 0.52012 (41618) SS BOND : bond 0.00409 ( 43) SS BOND : angle 1.68505 ( 86) hydrogen bonds : bond 0.04501 ( 1076) hydrogen bonds : angle 5.29997 ( 2994) link_BETA1-4 : bond 0.00346 ( 18) link_BETA1-4 : angle 1.00410 ( 54) link_NAG-ASN : bond 0.00429 ( 45) link_NAG-ASN : angle 2.77204 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 123 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7399 (m) REVERT: A 733 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8103 (ttpp) REVERT: B 117 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8140 (tt) REVERT: C 342 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7021 (t80) REVERT: E 79 MET cc_start: 0.0011 (pmm) cc_final: -0.0260 (pmm) REVERT: G 79 MET cc_start: 0.0053 (pmm) cc_final: -0.0269 (pmm) REVERT: I 105 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7206 (tm-30) outliers start: 67 outliers final: 38 residues processed: 183 average time/residue: 0.1877 time to fit residues: 57.6454 Evaluate side-chains 159 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 163 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 361 optimal weight: 30.0000 chunk 234 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 350 optimal weight: 0.4980 chunk 275 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.159900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.109201 restraints weight = 70241.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108730 restraints weight = 43955.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107654 restraints weight = 33915.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.108097 restraints weight = 32996.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109023 restraints weight = 27410.473| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 30669 Z= 0.171 Angle : 0.573 11.912 41893 Z= 0.286 Chirality : 0.045 0.515 4944 Planarity : 0.004 0.052 5287 Dihedral : 5.533 58.420 5353 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.88 % Rotamer: Outliers : 3.31 % Allowed : 15.78 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.14), residues: 3709 helix: 1.96 (0.21), residues: 673 sheet: 0.14 (0.17), residues: 959 loop : -1.13 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.021 0.001 TYR I 102 PHE 0.018 0.001 PHE C 377 TRP 0.012 0.001 TRP C 104 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00411 (30563) covalent geometry : angle 0.54616 (41618) SS BOND : bond 0.00404 ( 43) SS BOND : angle 1.63770 ( 86) hydrogen bonds : bond 0.04619 ( 1076) hydrogen bonds : angle 5.20693 ( 2994) link_BETA1-4 : bond 0.00340 ( 18) link_BETA1-4 : angle 1.09842 ( 54) link_NAG-ASN : bond 0.00433 ( 45) link_NAG-ASN : angle 2.77819 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 130 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 VAL cc_start: 0.7719 (OUTLIER) cc_final: 0.7402 (m) REVERT: A 568 ASP cc_start: 0.7593 (t0) cc_final: 0.7362 (t0) REVERT: A 733 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8032 (ttpp) REVERT: A 878 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8675 (tt) REVERT: A 912 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8699 (p) REVERT: B 117 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8062 (tt) REVERT: C 342 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7040 (t80) REVERT: E 79 MET cc_start: -0.0129 (pmm) cc_final: -0.0379 (pmm) REVERT: G 79 MET cc_start: -0.0270 (pmm) cc_final: -0.0530 (pmm) REVERT: I 30 ARG cc_start: 0.8724 (tpp80) cc_final: 0.8237 (mmp80) REVERT: I 105 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7283 (tm-30) outliers start: 106 outliers final: 65 residues processed: 229 average time/residue: 0.1824 time to fit residues: 70.8083 Evaluate side-chains 194 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 122 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 71 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 341 optimal weight: 6.9990 chunk 308 optimal weight: 7.9990 chunk 134 optimal weight: 30.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.158511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.105861 restraints weight = 70464.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105709 restraints weight = 46181.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.105727 restraints weight = 33619.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.106009 restraints weight = 32200.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.106459 restraints weight = 27832.422| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 30669 Z= 0.259 Angle : 0.653 15.586 41893 Z= 0.324 Chirality : 0.047 0.533 4944 Planarity : 0.004 0.065 5287 Dihedral : 5.573 53.216 5353 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 3.78 % Allowed : 16.62 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: -0.50 (0.14), residues: 3709 helix: 1.70 (0.21), residues: 677 sheet: 0.01 (0.17), residues: 956 loop : -1.23 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 34 TYR 0.028 0.002 TYR B 369 PHE 0.018 0.002 PHE A 92 TRP 0.014 0.001 TRP B 152 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00624 (30563) covalent geometry : angle 0.62522 (41618) SS BOND : bond 0.00503 ( 43) SS BOND : angle 1.83475 ( 86) hydrogen bonds : bond 0.05301 ( 1076) hydrogen bonds : angle 5.31417 ( 2994) link_BETA1-4 : bond 0.00320 ( 18) link_BETA1-4 : angle 1.10463 ( 54) link_NAG-ASN : bond 0.00479 ( 45) link_NAG-ASN : angle 3.03234 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 132 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: A 733 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8102 (ttpp) REVERT: A 878 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8586 (tt) REVERT: A 912 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8854 (p) REVERT: B 117 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8230 (tt) REVERT: C 58 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8058 (m-10) REVERT: C 342 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7224 (t80) REVERT: C 408 ARG cc_start: 0.8944 (mtm110) cc_final: 0.8679 (ptt180) REVERT: C 759 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7859 (t80) REVERT: I 30 ARG cc_start: 0.8788 (tpp80) cc_final: 0.8306 (mmp80) REVERT: I 79 MET cc_start: -0.0760 (mpp) cc_final: -0.0995 (mpp) REVERT: I 105 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7347 (tm-30) outliers start: 121 outliers final: 87 residues processed: 244 average time/residue: 0.1828 time to fit residues: 74.9104 Evaluate side-chains 218 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 122 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 117 optimal weight: 2.9990 chunk 357 optimal weight: 50.0000 chunk 194 optimal weight: 0.8980 chunk 232 optimal weight: 9.9990 chunk 281 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 370 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.160333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.108435 restraints weight = 70148.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.108768 restraints weight = 42077.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.108615 restraints weight = 34649.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109495 restraints weight = 26766.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109646 restraints weight = 24156.665| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30669 Z= 0.115 Angle : 0.553 12.650 41893 Z= 0.275 Chirality : 0.044 0.470 4944 Planarity : 0.003 0.052 5287 Dihedral : 5.126 48.265 5353 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 2.62 % Allowed : 17.74 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.14), residues: 3709 helix: 2.00 (0.21), residues: 672 sheet: 0.18 (0.17), residues: 948 loop : -1.15 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.020 0.001 TYR E 102 PHE 0.014 0.001 PHE A 238 TRP 0.014 0.001 TRP C 104 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00264 (30563) covalent geometry : angle 0.52760 (41618) SS BOND : bond 0.00404 ( 43) SS BOND : angle 1.38752 ( 86) hydrogen bonds : bond 0.04260 ( 1076) hydrogen bonds : angle 5.02615 ( 2994) link_BETA1-4 : bond 0.00370 ( 18) link_BETA1-4 : angle 1.03313 ( 54) link_NAG-ASN : bond 0.00429 ( 45) link_NAG-ASN : angle 2.71454 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 138 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6587 (mp) REVERT: A 733 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7907 (ttpp) REVERT: B 117 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8014 (tt) REVERT: B 432 CYS cc_start: 0.5181 (OUTLIER) cc_final: 0.3595 (p) REVERT: C 342 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7259 (t80) REVERT: C 553 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8553 (p) REVERT: C 902 MET cc_start: 0.8825 (tpp) cc_final: 0.8328 (tpt) REVERT: I 30 ARG cc_start: 0.8772 (tpp80) cc_final: 0.8276 (mmp80) REVERT: I 105 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7325 (tm-30) outliers start: 84 outliers final: 59 residues processed: 211 average time/residue: 0.1873 time to fit residues: 66.1155 Evaluate side-chains 190 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 124 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 13 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 369 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.159799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.110735 restraints weight = 70131.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109414 restraints weight = 42177.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108123 restraints weight = 37353.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.108803 restraints weight = 33777.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109509 restraints weight = 27906.575| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30669 Z= 0.131 Angle : 0.560 12.789 41893 Z= 0.276 Chirality : 0.044 0.467 4944 Planarity : 0.003 0.052 5287 Dihedral : 4.894 46.178 5353 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.71 % Rotamer: Outliers : 2.91 % Allowed : 17.84 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.14), residues: 3709 helix: 2.02 (0.21), residues: 674 sheet: 0.20 (0.17), residues: 968 loop : -1.11 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.018 0.001 TYR C1067 PHE 0.018 0.001 PHE C 392 TRP 0.012 0.001 TRP C 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00311 (30563) covalent geometry : angle 0.53479 (41618) SS BOND : bond 0.00409 ( 43) SS BOND : angle 1.42760 ( 86) hydrogen bonds : bond 0.04205 ( 1076) hydrogen bonds : angle 4.94890 ( 2994) link_BETA1-4 : bond 0.00354 ( 18) link_BETA1-4 : angle 1.02069 ( 54) link_NAG-ASN : bond 0.00417 ( 45) link_NAG-ASN : angle 2.70602 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 126 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6587 (mp) REVERT: A 503 VAL cc_start: 0.7758 (OUTLIER) cc_final: 0.7477 (m) REVERT: A 733 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7876 (ttpp) REVERT: B 117 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8002 (tt) REVERT: B 432 CYS cc_start: 0.5308 (OUTLIER) cc_final: 0.3793 (p) REVERT: C 342 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7338 (t80) REVERT: C 553 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8551 (p) REVERT: C 759 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7488 (t80) REVERT: C 902 MET cc_start: 0.8763 (tpp) cc_final: 0.8402 (tpt) REVERT: C 1017 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7860 (tm-30) REVERT: I 30 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8263 (mmp80) REVERT: I 79 MET cc_start: -0.0548 (mpp) cc_final: -0.0825 (mpp) REVERT: I 105 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7311 (tm-30) outliers start: 93 outliers final: 70 residues processed: 206 average time/residue: 0.1841 time to fit residues: 63.2208 Evaluate side-chains 202 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 123 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 82 optimal weight: 10.0000 chunk 330 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 302 optimal weight: 0.0980 chunk 344 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 246 optimal weight: 0.0030 chunk 364 optimal weight: 40.0000 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.161360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110099 restraints weight = 70355.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.110660 restraints weight = 43605.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.109920 restraints weight = 31821.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110401 restraints weight = 30244.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110861 restraints weight = 26577.081| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30669 Z= 0.118 Angle : 0.547 12.676 41893 Z= 0.270 Chirality : 0.044 0.452 4944 Planarity : 0.003 0.052 5287 Dihedral : 4.585 45.419 5353 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.20 % Rotamer: Outliers : 2.62 % Allowed : 18.18 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.14), residues: 3709 helix: 2.07 (0.21), residues: 672 sheet: 0.20 (0.17), residues: 972 loop : -1.04 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.018 0.001 TYR C1067 PHE 0.025 0.001 PHE A 565 TRP 0.012 0.001 TRP C 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00277 (30563) covalent geometry : angle 0.52370 (41618) SS BOND : bond 0.00415 ( 43) SS BOND : angle 1.30637 ( 86) hydrogen bonds : bond 0.03977 ( 1076) hydrogen bonds : angle 4.85338 ( 2994) link_BETA1-4 : bond 0.00357 ( 18) link_BETA1-4 : angle 1.00303 ( 54) link_NAG-ASN : bond 0.00427 ( 45) link_NAG-ASN : angle 2.63491 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 134 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6599 (mp) REVERT: A 503 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7574 (m) REVERT: A 733 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7734 (ttpp) REVERT: A 912 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8723 (p) REVERT: B 117 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7862 (tt) REVERT: C 342 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7399 (t80) REVERT: C 553 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8524 (p) REVERT: C 759 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7526 (t80) REVERT: C 902 MET cc_start: 0.8689 (tpp) cc_final: 0.8390 (tpt) REVERT: C 1017 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7882 (tm-30) REVERT: I 79 MET cc_start: -0.0609 (mpp) cc_final: -0.0919 (mpp) REVERT: I 105 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7357 (tm-30) outliers start: 84 outliers final: 64 residues processed: 207 average time/residue: 0.1779 time to fit residues: 61.3933 Evaluate side-chains 196 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 123 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 156 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 216 optimal weight: 0.8980 chunk 289 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 302 optimal weight: 0.0980 chunk 320 optimal weight: 40.0000 chunk 130 optimal weight: 5.9990 chunk 312 optimal weight: 30.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.160850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112195 restraints weight = 70003.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.110857 restraints weight = 42294.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.109727 restraints weight = 36826.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110331 restraints weight = 33115.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.111158 restraints weight = 27534.694| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30669 Z= 0.107 Angle : 0.556 13.096 41893 Z= 0.273 Chirality : 0.044 0.443 4944 Planarity : 0.003 0.055 5287 Dihedral : 4.445 44.843 5353 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 2.28 % Allowed : 18.84 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.14), residues: 3709 helix: 2.17 (0.22), residues: 670 sheet: 0.26 (0.17), residues: 974 loop : -1.02 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.017 0.001 TYR C1067 PHE 0.028 0.001 PHE C 377 TRP 0.012 0.001 TRP C 104 HIS 0.001 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00248 (30563) covalent geometry : angle 0.53371 (41618) SS BOND : bond 0.00403 ( 43) SS BOND : angle 1.30141 ( 86) hydrogen bonds : bond 0.03830 ( 1076) hydrogen bonds : angle 4.79485 ( 2994) link_BETA1-4 : bond 0.00373 ( 18) link_BETA1-4 : angle 0.99997 ( 54) link_NAG-ASN : bond 0.00425 ( 45) link_NAG-ASN : angle 2.59850 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7418 Ramachandran restraints generated. 3709 Oldfield, 0 Emsley, 3709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 133 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6567 (mp) REVERT: A 503 VAL cc_start: 0.7816 (OUTLIER) cc_final: 0.7526 (m) REVERT: A 912 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 104 TRP cc_start: 0.7760 (m-90) cc_final: 0.7512 (m-90) REVERT: B 117 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7891 (tt) REVERT: C 342 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7401 (t80) REVERT: C 553 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8589 (p) REVERT: C 759 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7545 (t80) REVERT: C 902 MET cc_start: 0.8694 (tpp) cc_final: 0.8413 (tpt) REVERT: I 79 MET cc_start: -0.0626 (mpp) cc_final: -0.0961 (mpp) REVERT: I 105 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7307 (tm-30) outliers start: 73 outliers final: 60 residues processed: 194 average time/residue: 0.1893 time to fit residues: 61.2072 Evaluate side-chains 197 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 129 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 chunk 322 optimal weight: 50.0000 chunk 212 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 182 optimal weight: 0.9990 chunk 353 optimal weight: 7.9990 chunk 279 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.157883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.112873 restraints weight = 64991.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.109702 restraints weight = 40187.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.110316 restraints weight = 37192.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.109959 restraints weight = 29723.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.110078 restraints weight = 25794.980| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30669 Z= 0.113 Angle : 0.557 12.939 41893 Z= 0.274 Chirality : 0.044 0.440 4944 Planarity : 0.003 0.055 5287 Dihedral : 4.320 43.964 5353 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 2.53 % Allowed : 18.65 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.14), residues: 3709 helix: 2.20 (0.21), residues: 670 sheet: 0.25 (0.17), residues: 975 loop : -0.99 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 567 TYR 0.017 0.001 TYR C1067 PHE 0.023 0.001 PHE A 565 TRP 0.012 0.001 TRP C 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00265 (30563) covalent geometry : angle 0.53513 (41618) SS BOND : bond 0.00389 ( 43) SS BOND : angle 1.24110 ( 86) hydrogen bonds : bond 0.03823 ( 1076) hydrogen bonds : angle 4.74874 ( 2994) link_BETA1-4 : bond 0.00362 ( 18) link_BETA1-4 : angle 0.99633 ( 54) link_NAG-ASN : bond 0.00421 ( 45) link_NAG-ASN : angle 2.58358 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5497.33 seconds wall clock time: 95 minutes 54.88 seconds (5754.88 seconds total)