Starting phenix.real_space_refine on Thu Jun 26 00:28:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8heb_34686/06_2025/8heb_34686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8heb_34686/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8heb_34686/06_2025/8heb_34686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8heb_34686/06_2025/8heb_34686.map" model { file = "/net/cci-nas-00/data/ceres_data/8heb_34686/06_2025/8heb_34686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8heb_34686/06_2025/8heb_34686.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 2, '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: {'GLN:plan1': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP: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: 19.27, per 1000 atoms: 0.64 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: 7.91 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 5.02 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: 15.26 Time building geometry restraints manager: 9.41 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 \ 1147 or resid 1301 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 1147 or resid 13 \ 01 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 1147 or resid 1301 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: 23.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.410 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 79.230 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.530 ------------------------------------------------------------------------------- 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 : 6.58 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (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 TRP 0.011 0.001 TRP A 104 HIS 0.002 0.000 HIS I 55 PHE 0.024 0.001 PHE A 201 TYR 0.019 0.001 TYR C 369 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 45) link_NAG-ASN : angle 2.88015 ( 135) link_BETA1-4 : bond 0.00358 ( 18) link_BETA1-4 : angle 1.09669 ( 54) hydrogen bonds : bond 0.23448 ( 1076) hydrogen bonds : angle 8.22722 ( 2994) SS BOND : bond 0.00372 ( 43) SS BOND : angle 1.07756 ( 86) covalent geometry : bond 0.00357 (30563) covalent geometry : angle 0.57257 (41618) *********************** 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 : 3.289 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: 0.4539 time to fit residues: 100.5466 Evaluate side-chains 127 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 3.097 ------------------------------------------------------------------------------- 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 314 optimal weight: 30.0000 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 292 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 177 optimal weight: 0.0970 chunk 217 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.159708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.109586 restraints weight = 69729.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109091 restraints weight = 42063.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108444 restraints weight = 32967.791| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0804 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= 0.127 Angle : 0.557 13.271 41893 Z= 0.285 Chirality : 0.045 0.471 4944 Planarity : 0.004 0.049 5287 Dihedral : 6.638 59.804 5353 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.82 % Rotamer: Outliers : 1.84 % Allowed : 13.37 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3709 helix: 2.10 (0.21), residues: 680 sheet: 0.23 (0.17), residues: 947 loop : -1.03 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 104 HIS 0.003 0.001 HIS I 55 PHE 0.012 0.001 PHE C 238 TYR 0.021 0.001 TYR A1067 ARG 0.007 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 45) link_NAG-ASN : angle 2.70941 ( 135) link_BETA1-4 : bond 0.00396 ( 18) link_BETA1-4 : angle 0.96315 ( 54) hydrogen bonds : bond 0.04863 ( 1076) hydrogen bonds : angle 5.94314 ( 2994) SS BOND : bond 0.00416 ( 43) SS BOND : angle 1.13086 ( 86) covalent geometry : bond 0.00287 (30563) covalent geometry : angle 0.53319 (41618) *********************** 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 198 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 3.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 503 VAL cc_start: 0.7713 (OUTLIER) cc_final: 0.7413 (m) REVERT: B 117 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7919 (tt) REVERT: E 30 ARG cc_start: 0.8496 (tpp80) cc_final: 0.8045 (mmp80) REVERT: G 30 ARG cc_start: 0.8458 (tpp80) cc_final: 0.7993 (mmp80) REVERT: G 79 MET cc_start: -0.0406 (pmm) cc_final: -0.0725 (pmm) REVERT: I 30 ARG cc_start: 0.8501 (tpp80) cc_final: 0.8037 (mmp80) REVERT: I 105 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7019 (tm-30) outliers start: 59 outliers final: 29 residues processed: 191 average time/residue: 0.4503 time to fit residues: 146.1727 Evaluate side-chains 159 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 3.252 ------------------------------------------------------------------------------- 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 745 ASP 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 72 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 366 optimal weight: 40.0000 chunk 322 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 344 optimal weight: 40.0000 chunk 364 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.159220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.104091 restraints weight = 71197.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.105657 restraints weight = 48978.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105773 restraints weight = 32354.394| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 30669 Z= 0.301 Angle : 0.687 15.235 41893 Z= 0.346 Chirality : 0.048 0.505 4944 Planarity : 0.004 0.075 5287 Dihedral : 6.477 59.805 5353 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.77 % Rotamer: Outliers : 2.97 % Allowed : 15.00 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3709 helix: 1.71 (0.21), residues: 676 sheet: 0.05 (0.17), residues: 955 loop : -1.25 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.005 0.001 HIS B1088 PHE 0.019 0.002 PHE A 92 TYR 0.032 0.002 TYR B 170 ARG 0.005 0.000 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 45) link_NAG-ASN : angle 3.14101 ( 135) link_BETA1-4 : bond 0.00342 ( 18) link_BETA1-4 : angle 1.13472 ( 54) hydrogen bonds : bond 0.05956 ( 1076) hydrogen bonds : angle 5.72425 ( 2994) SS BOND : bond 0.00486 ( 43) SS BOND : angle 1.95676 ( 86) covalent geometry : bond 0.00726 (30563) covalent geometry : angle 0.65798 (41618) *********************** 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 219 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 124 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.9275 (mp) cc_final: 0.9037 (tt) REVERT: A 733 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8175 (ttpp) REVERT: A 779 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8571 (tm-30) REVERT: B 117 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8217 (tt) REVERT: C 342 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.6966 (t80) REVERT: C 759 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7887 (t80) REVERT: C 913 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8832 (pt0) REVERT: E 79 MET cc_start: -0.0203 (pmm) cc_final: -0.0490 (pmm) REVERT: G 79 MET cc_start: -0.0245 (pmm) cc_final: -0.0571 (pmm) REVERT: I 30 ARG cc_start: 0.8646 (tpp80) cc_final: 0.8187 (mmp80) REVERT: I 105 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7105 (tm-30) outliers start: 95 outliers final: 58 residues processed: 211 average time/residue: 0.4821 time to fit residues: 173.3235 Evaluate side-chains 180 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 116 time to evaluate : 3.103 ------------------------------------------------------------------------------- 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 729 VAL 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 915 VAL Chi-restraints excluded: chain A residue 961 THR 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 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 705 VAL Chi-restraints excluded: chain C residue 745 ASP 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 913 GLN 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 223 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 275 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 244 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.0060 chunk 192 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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** C 207 HIS D 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.156253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.113880 restraints weight = 65315.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.112148 restraints weight = 45433.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.111358 restraints weight = 46975.805| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 30669 Z= 0.106 Angle : 0.536 13.402 41893 Z= 0.271 Chirality : 0.044 0.439 4944 Planarity : 0.003 0.051 5287 Dihedral : 5.805 59.729 5353 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.41 % Rotamer: Outliers : 2.06 % Allowed : 16.68 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3709 helix: 2.05 (0.21), residues: 671 sheet: 0.18 (0.17), residues: 959 loop : -1.13 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.002 0.000 HIS C1088 PHE 0.013 0.001 PHE C 238 TYR 0.024 0.001 TYR I 102 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 45) link_NAG-ASN : angle 2.74614 ( 135) link_BETA1-4 : bond 0.00375 ( 18) link_BETA1-4 : angle 0.99292 ( 54) hydrogen bonds : bond 0.04390 ( 1076) hydrogen bonds : angle 5.27531 ( 2994) SS BOND : bond 0.00535 ( 43) SS BOND : angle 1.52767 ( 86) covalent geometry : bond 0.00232 (30563) covalent geometry : angle 0.50855 (41618) *********************** 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 199 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 133 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7397 (m) REVERT: A 733 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8135 (ttpp) REVERT: B 117 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8269 (tt) REVERT: C 342 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.6981 (t80) REVERT: E 79 MET cc_start: 0.0101 (pmm) cc_final: -0.0198 (pmm) REVERT: G 79 MET cc_start: 0.0152 (pmm) cc_final: -0.0177 (pmm) REVERT: I 105 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7085 (tm-30) outliers start: 66 outliers final: 33 residues processed: 191 average time/residue: 0.3964 time to fit residues: 128.0405 Evaluate side-chains 159 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 3.277 ------------------------------------------------------------------------------- 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 611 LEU 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 B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU 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 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 745 ASP 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 277 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 268 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 310 optimal weight: 50.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.159229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106904 restraints weight = 70137.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.106776 restraints weight = 43642.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106661 restraints weight = 35215.552| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 30669 Z= 0.231 Angle : 0.621 13.014 41893 Z= 0.310 Chirality : 0.046 0.562 4944 Planarity : 0.004 0.055 5287 Dihedral : 5.674 57.223 5353 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.04 % Rotamer: Outliers : 3.31 % Allowed : 16.06 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3709 helix: 1.86 (0.21), residues: 673 sheet: 0.11 (0.17), residues: 954 loop : -1.21 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS B1088 PHE 0.017 0.002 PHE B1121 TYR 0.024 0.001 TYR B 170 ARG 0.003 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 45) link_NAG-ASN : angle 2.91296 ( 135) link_BETA1-4 : bond 0.00302 ( 18) link_BETA1-4 : angle 1.10602 ( 54) hydrogen bonds : bond 0.05057 ( 1076) hydrogen bonds : angle 5.30979 ( 2994) SS BOND : bond 0.00523 ( 43) SS BOND : angle 1.79024 ( 86) covalent geometry : bond 0.00556 (30563) covalent geometry : angle 0.59419 (41618) *********************** 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 235 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 129 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7451 (m) REVERT: A 733 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8063 (ttpp) REVERT: A 878 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8517 (tt) REVERT: A 912 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8813 (p) REVERT: B 117 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8142 (tt) REVERT: C 342 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.6940 (t80) REVERT: E 79 MET cc_start: -0.0099 (pmm) cc_final: -0.0384 (pmm) REVERT: G 79 MET cc_start: -0.0273 (pmm) cc_final: -0.0477 (pmm) REVERT: I 30 ARG cc_start: 0.8755 (tpp80) cc_final: 0.8276 (mmp80) REVERT: I 105 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7331 (tm-30) outliers start: 106 outliers final: 65 residues processed: 224 average time/residue: 0.3877 time to fit residues: 147.8599 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 : 3.275 ------------------------------------------------------------------------------- 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 733 LYS Chi-restraints excluded: chain A residue 761 THR 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 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 338 PHE Chi-restraints excluded: chain B residue 393 THR 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 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 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 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 745 ASP 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 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 F residue 18 VAL Chi-restraints excluded: chain G residue 47 ILE 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 12 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 328 optimal weight: 50.0000 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 336 optimal weight: 40.0000 chunk 144 optimal weight: 0.4980 chunk 366 optimal weight: 30.0000 chunk 180 optimal weight: 0.5980 chunk 283 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.159713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107412 restraints weight = 70186.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108250 restraints weight = 46365.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108459 restraints weight = 31292.884| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30669 Z= 0.138 Angle : 0.560 13.222 41893 Z= 0.277 Chirality : 0.044 0.500 4944 Planarity : 0.003 0.052 5287 Dihedral : 5.358 54.329 5353 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 2.91 % Allowed : 16.99 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3709 helix: 2.04 (0.21), residues: 673 sheet: 0.13 (0.17), residues: 958 loop : -1.14 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.002 0.000 HIS B1064 PHE 0.015 0.001 PHE C 392 TYR 0.023 0.001 TYR B 369 ARG 0.003 0.000 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 45) link_NAG-ASN : angle 2.77696 ( 135) link_BETA1-4 : bond 0.00355 ( 18) link_BETA1-4 : angle 1.02836 ( 54) hydrogen bonds : bond 0.04418 ( 1076) hydrogen bonds : angle 5.11347 ( 2994) SS BOND : bond 0.00421 ( 43) SS BOND : angle 1.54281 ( 86) covalent geometry : bond 0.00326 (30563) covalent geometry : angle 0.53295 (41618) *********************** 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 225 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 132 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.8217 (m-80) REVERT: A 733 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7982 (ttpp) REVERT: B 117 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8032 (tt) REVERT: B 369 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: C 342 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7094 (t80) REVERT: C 902 MET cc_start: 0.8813 (tpp) cc_final: 0.8386 (tpt) REVERT: I 30 ARG cc_start: 0.8793 (tpp80) cc_final: 0.8304 (mmp80) REVERT: I 79 MET cc_start: -0.0403 (pmm) cc_final: -0.0672 (pmm) REVERT: I 105 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7343 (tm-30) outliers start: 93 outliers final: 58 residues processed: 215 average time/residue: 0.4004 time to fit residues: 145.4065 Evaluate side-chains 187 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 123 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR 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 733 LYS Chi-restraints excluded: chain A residue 785 VAL 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 338 PHE Chi-restraints excluded: chain B residue 369 TYR 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 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 131 CYS 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 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 745 ASP 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 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 349 optimal weight: 8.9990 chunk 74 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 337 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 202 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.161052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109791 restraints weight = 70525.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.110121 restraints weight = 43925.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.109845 restraints weight = 32048.417| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30669 Z= 0.110 Angle : 0.533 12.310 41893 Z= 0.265 Chirality : 0.044 0.464 4944 Planarity : 0.003 0.052 5287 Dihedral : 4.909 48.724 5353 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.69 % Rotamer: Outliers : 2.66 % Allowed : 17.28 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3709 helix: 2.22 (0.22), residues: 671 sheet: 0.25 (0.17), residues: 948 loop : -1.07 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.001 0.000 HIS A 207 PHE 0.015 0.001 PHE C 392 TYR 0.021 0.001 TYR I 102 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 45) link_NAG-ASN : angle 2.65433 ( 135) link_BETA1-4 : bond 0.00385 ( 18) link_BETA1-4 : angle 1.00666 ( 54) hydrogen bonds : bond 0.03995 ( 1076) hydrogen bonds : angle 4.91161 ( 2994) SS BOND : bond 0.00372 ( 43) SS BOND : angle 1.31832 ( 86) covalent geometry : bond 0.00254 (30563) covalent geometry : angle 0.50831 (41618) *********************** 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 227 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 142 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6606 (mp) REVERT: A 503 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7390 (m) REVERT: A 912 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8698 (p) REVERT: B 117 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7965 (tt) REVERT: C 342 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7124 (t80) REVERT: C 553 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8580 (p) REVERT: C 759 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7412 (t80) REVERT: C 902 MET cc_start: 0.8729 (tpp) cc_final: 0.8471 (tpt) REVERT: I 30 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8280 (mmp80) REVERT: I 79 MET cc_start: -0.0325 (pmm) cc_final: -0.0572 (pmm) REVERT: I 105 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7321 (tm-30) outliers start: 85 outliers final: 56 residues processed: 215 average time/residue: 0.4047 time to fit residues: 145.8476 Evaluate side-chains 191 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 127 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 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 785 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1129 VAL 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 241 LEU Chi-restraints excluded: chain B residue 338 PHE 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 588 THR Chi-restraints excluded: chain B residue 595 VAL 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 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 318 PHE 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 649 CYS Chi-restraints excluded: chain C residue 745 ASP 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 948 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 209 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 314 optimal weight: 30.0000 chunk 213 optimal weight: 6.9990 chunk 306 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 348 optimal weight: 30.0000 chunk 323 optimal weight: 0.3980 chunk 263 optimal weight: 0.7980 chunk 286 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.161265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110430 restraints weight = 71114.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.110502 restraints weight = 43188.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.110140 restraints weight = 32718.751| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30669 Z= 0.110 Angle : 0.539 12.045 41893 Z= 0.267 Chirality : 0.044 0.453 4944 Planarity : 0.003 0.053 5287 Dihedral : 4.703 45.614 5353 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.20 % Rotamer: Outliers : 2.87 % Allowed : 17.40 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3709 helix: 2.19 (0.22), residues: 669 sheet: 0.29 (0.17), residues: 949 loop : -1.05 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.001 0.000 HIS A1088 PHE 0.033 0.001 PHE C 168 TYR 0.020 0.001 TYR B 369 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 45) link_NAG-ASN : angle 2.62293 ( 135) link_BETA1-4 : bond 0.00402 ( 18) link_BETA1-4 : angle 1.01534 ( 54) hydrogen bonds : bond 0.03896 ( 1076) hydrogen bonds : angle 4.85021 ( 2994) SS BOND : bond 0.00388 ( 43) SS BOND : angle 1.27630 ( 86) covalent geometry : bond 0.00253 (30563) covalent geometry : angle 0.51502 (41618) *********************** 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 225 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 133 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 VAL cc_start: 0.7456 (OUTLIER) cc_final: 0.7146 (m) REVERT: A 733 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7780 (ttpp) REVERT: A 912 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8658 (p) REVERT: B 117 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7920 (tt) REVERT: B 432 CYS cc_start: 0.5038 (OUTLIER) cc_final: 0.3364 (p) REVERT: C 342 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7224 (t80) REVERT: C 553 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8572 (p) REVERT: C 759 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7542 (t80) REVERT: C 902 MET cc_start: 0.8706 (tpp) cc_final: 0.8464 (tpt) REVERT: I 30 ARG cc_start: 0.8804 (tpp80) cc_final: 0.8275 (mmp80) REVERT: I 79 MET cc_start: -0.0218 (pmm) cc_final: -0.0464 (pmm) REVERT: I 105 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7336 (tm-30) outliers start: 92 outliers final: 70 residues processed: 213 average time/residue: 0.3990 time to fit residues: 143.6808 Evaluate side-chains 205 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 126 time to evaluate : 3.119 ------------------------------------------------------------------------------- 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 361 CYS 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 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 733 LYS Chi-restraints excluded: chain A residue 785 VAL 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 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 241 LEU 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 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 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 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 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 745 ASP 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 948 LEU 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 47 ILE 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 131 optimal weight: 40.0000 chunk 173 optimal weight: 2.9990 chunk 203 optimal weight: 0.0670 chunk 277 optimal weight: 1.9990 chunk 359 optimal weight: 9.9990 chunk 23 optimal weight: 0.0370 chunk 306 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 285 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.157799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.112279 restraints weight = 64668.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.108792 restraints weight = 40177.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.109631 restraints weight = 37161.141| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30669 Z= 0.117 Angle : 0.547 12.181 41893 Z= 0.270 Chirality : 0.044 0.448 4944 Planarity : 0.003 0.054 5287 Dihedral : 4.478 44.429 5353 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 2.59 % Allowed : 17.84 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3709 helix: 2.19 (0.21), residues: 670 sheet: 0.28 (0.17), residues: 966 loop : -1.00 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.002 0.000 HIS A1088 PHE 0.027 0.001 PHE C 168 TYR 0.021 0.001 TYR C 369 ARG 0.002 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 45) link_NAG-ASN : angle 2.61402 ( 135) link_BETA1-4 : bond 0.00358 ( 18) link_BETA1-4 : angle 1.00429 ( 54) hydrogen bonds : bond 0.03909 ( 1076) hydrogen bonds : angle 4.81491 ( 2994) SS BOND : bond 0.00392 ( 43) SS BOND : angle 1.25587 ( 86) covalent geometry : bond 0.00274 (30563) covalent geometry : angle 0.52393 (41618) *********************** 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 215 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 132 time to evaluate : 3.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6515 (mp) REVERT: A 503 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7230 (m) REVERT: A 733 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7894 (ttpp) REVERT: A 912 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8676 (p) REVERT: B 104 TRP cc_start: 0.7861 (m-90) cc_final: 0.7647 (m-90) REVERT: B 117 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8127 (tt) REVERT: C 342 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7197 (t80) REVERT: C 553 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8654 (p) REVERT: C 759 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7665 (t80) REVERT: C 902 MET cc_start: 0.8744 (tpp) cc_final: 0.8396 (tpt) REVERT: I 30 ARG cc_start: 0.8615 (tpp80) cc_final: 0.8104 (mmp80) REVERT: I 79 MET cc_start: -0.0159 (pmm) cc_final: -0.0369 (pmm) REVERT: I 105 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7288 (tm-30) outliers start: 83 outliers final: 71 residues processed: 204 average time/residue: 0.5042 time to fit residues: 175.0437 Evaluate side-chains 205 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 125 time to evaluate : 3.646 ------------------------------------------------------------------------------- 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 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 733 LYS Chi-restraints excluded: chain A residue 785 VAL 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 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 241 LEU 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 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 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 318 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 393 THR 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 745 ASP 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 948 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 334 optimal weight: 30.0000 chunk 178 optimal weight: 0.6980 chunk 318 optimal weight: 40.0000 chunk 64 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 144 optimal weight: 0.0170 chunk 234 optimal weight: 3.9990 chunk 202 optimal weight: 0.0020 chunk 344 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.1430 ------------------------------------------------------------------------------- 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** B 690 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.160859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112236 restraints weight = 70722.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.110823 restraints weight = 43440.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109884 restraints weight = 35537.351| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30669 Z= 0.128 Angle : 0.560 12.330 41893 Z= 0.275 Chirality : 0.044 0.448 4944 Planarity : 0.003 0.054 5287 Dihedral : 4.381 44.020 5353 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.93 % Rotamer: Outliers : 2.62 % Allowed : 17.99 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3709 helix: 2.17 (0.21), residues: 671 sheet: 0.26 (0.17), residues: 982 loop : -0.97 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.002 0.000 HIS B1088 PHE 0.026 0.001 PHE C 168 TYR 0.017 0.001 TYR B1067 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 45) link_NAG-ASN : angle 2.61306 ( 135) link_BETA1-4 : bond 0.00346 ( 18) link_BETA1-4 : angle 1.00343 ( 54) hydrogen bonds : bond 0.03992 ( 1076) hydrogen bonds : angle 4.80117 ( 2994) SS BOND : bond 0.00399 ( 43) SS BOND : angle 1.25302 ( 86) covalent geometry : bond 0.00303 (30563) covalent geometry : angle 0.53779 (41618) ********************** 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 214 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 130 time to evaluate : 6.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6593 (mp) REVERT: A 503 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7282 (m) REVERT: A 733 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7853 (ttpp) REVERT: A 912 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8436 (p) REVERT: B 117 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7979 (tt) REVERT: C 342 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7331 (t80) REVERT: C 553 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8614 (p) REVERT: C 759 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7650 (t80) REVERT: C 902 MET cc_start: 0.8705 (tpp) cc_final: 0.8193 (tpt) REVERT: C 1017 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7756 (tm-30) REVERT: I 30 ARG cc_start: 0.8756 (tpp80) cc_final: 0.8203 (mmp80) REVERT: I 79 MET cc_start: -0.0322 (pmm) cc_final: -0.0541 (pmm) REVERT: I 105 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7290 (tm-30) outliers start: 84 outliers final: 70 residues processed: 203 average time/residue: 0.4795 time to fit residues: 170.1134 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 : 3.293 ------------------------------------------------------------------------------- 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 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 733 LYS Chi-restraints excluded: chain A residue 785 VAL 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 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 241 LEU 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 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 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 318 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 393 THR 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 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 745 ASP 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 948 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 76 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 191 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 359 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 366 optimal weight: 30.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.160991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111589 restraints weight = 70489.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.111104 restraints weight = 43572.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110021 restraints weight = 34118.244| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30669 Z= 0.123 Angle : 0.560 12.882 41893 Z= 0.275 Chirality : 0.044 0.445 4944 Planarity : 0.003 0.054 5287 Dihedral : 4.332 44.083 5353 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 2.53 % Allowed : 18.31 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3709 helix: 2.22 (0.21), residues: 671 sheet: 0.27 (0.17), residues: 981 loop : -0.96 (0.14), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.002 0.000 HIS A1088 PHE 0.026 0.001 PHE C 168 TYR 0.017 0.001 TYR B1067 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 45) link_NAG-ASN : angle 2.59692 ( 135) link_BETA1-4 : bond 0.00355 ( 18) link_BETA1-4 : angle 1.00101 ( 54) hydrogen bonds : bond 0.03931 ( 1076) hydrogen bonds : angle 4.76852 ( 2994) SS BOND : bond 0.00390 ( 43) SS BOND : angle 1.31079 ( 86) covalent geometry : bond 0.00291 (30563) covalent geometry : angle 0.53736 (41618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10594.58 seconds wall clock time: 193 minutes 20.14 seconds (11600.14 seconds total)