Starting phenix.real_space_refine on Thu Jun 26 02:26:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hec_34687/06_2025/8hec_34687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hec_34687/06_2025/8hec_34687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hec_34687/06_2025/8hec_34687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hec_34687/06_2025/8hec_34687.map" model { file = "/net/cci-nas-00/data/ceres_data/8hec_34687/06_2025/8hec_34687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hec_34687/06_2025/8hec_34687.cif" } resolution = 3.5 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= -0.001 sd= 0.037 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 18999 2.51 5 N 4894 2.21 5 O 5891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 2.87s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29925 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8000 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 51, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7992 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 51, 'TRANS': 976} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7985 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 51, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 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: 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: 21.41, per 1000 atoms: 0.72 Number of scatterers: 29925 At special positions: 0 Unit cell: (146.78, 156.62, 223.86, 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 5891 8.00 N 4894 7.00 C 18999 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 92 " distance=2.04 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=2.04 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-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 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 8.32 Conformation dependent library (CDL) restraints added in 4.0 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: 68 helices and 66 sheets defined 21.1% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.607A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.179A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.973A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.556A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 removed outlier: 3.642A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.776A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.799A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.728A 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 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.178A 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: 4.819A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.657A 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.326A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.647A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.551A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.045A 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 removed outlier: 3.659A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.685A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.560A 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: 4.117A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.575A 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 918 removed outlier: 4.090A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.292A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.125A 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: 3.617A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.164A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.027A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.785A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.705A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.262A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.605A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.189A 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 removed outlier: 3.725A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) 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 761 through 783 removed outlier: 3.538A 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 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.528A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.197A 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: 4.811A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.653A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.531A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.277A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.799A pdb=" N ALA D 82 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.860A pdb=" N ALA F 82 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 removed outlier: 3.505A pdb=" N ARG G 30 " --> pdb=" O SER G 27 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.678A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.979A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.608A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 142 removed outlier: 10.776A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.451A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.678A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.890A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 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 660 removed outlier: 5.882A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.093A 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 711 through 728 removed outlier: 6.859A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.641A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.736A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.834A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 132 through 134 removed outlier: 3.689A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.631A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.260A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.095A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.902A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.979A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.476A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.871A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.937A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 132 through 135 removed outlier: 4.180A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.947A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.269A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.691A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 540 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 659 removed outlier: 6.077A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.612A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 719 removed outlier: 6.458A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 717 through 719 removed outlier: 6.458A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.428A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.836A pdb=" N HIS D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.682A pdb=" N VAL D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 12 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 110 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 47 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.682A pdb=" N VAL D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 12 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 110 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY D 89 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA D 100 " --> pdb=" O GLY D 89 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.866A pdb=" N LEU E 17 " --> pdb=" O MET E 79 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.938A pdb=" N MET E 33 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TRP E 35 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.869A pdb=" N PHE E 106 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.719A pdb=" N HIS F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.830A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.830A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY F 89 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 100 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AG5, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.596A pdb=" N LEU G 17 " --> pdb=" O MET G 79 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 10 through 11 removed outlier: 7.157A pdb=" N MET G 33 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.724A pdb=" N HIS H 69 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.650A 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: 3.602A pdb=" N LYS H 110 " --> pdb=" O ALA H 12 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.650A 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: 3.602A pdb=" N LYS H 110 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY H 89 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA H 100 " --> pdb=" O GLY H 89 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AH2, first strand: chain 'I' and resid 2 through 6 Processing sheet with id=AH3, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.643A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3042 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: 16.26 Time building geometry restraints manager: 9.60 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: 9523 1.35 - 1.47: 7843 1.47 - 1.59: 13039 1.59 - 1.71: 0 1.71 - 1.83: 177 Bond restraints: 30582 Sorted by residual: bond pdb=" N GLY D 96 " pdb=" CA GLY D 96 " ideal model delta sigma weight residual 1.451 1.479 -0.029 8.60e-03 1.35e+04 1.10e+01 bond pdb=" N ASP D 97 " pdb=" CA ASP D 97 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.55e+00 bond pdb=" N SER F 94 " pdb=" CA SER F 94 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.16e+00 bond pdb=" N SER H 95 " pdb=" CA SER H 95 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.72e+00 bond pdb=" N SER F 95 " pdb=" CA SER F 95 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.23e-02 6.61e+03 5.52e+00 ... (remaining 30577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 40898 2.03 - 4.05: 678 4.05 - 6.08: 55 6.08 - 8.11: 4 8.11 - 10.13: 7 Bond angle restraints: 41642 Sorted by residual: angle pdb=" N ILE D 28 " pdb=" CA ILE D 28 " pdb=" C ILE D 28 " ideal model delta sigma weight residual 113.53 109.12 4.41 9.80e-01 1.04e+00 2.02e+01 angle pdb=" C SER F 92 " pdb=" CA SER F 92 " pdb=" CB SER F 92 " ideal model delta sigma weight residual 116.54 111.70 4.84 1.15e+00 7.56e-01 1.77e+01 angle pdb=" CA GLY D 96 " pdb=" C GLY D 96 " pdb=" O GLY D 96 " ideal model delta sigma weight residual 121.78 118.12 3.66 9.10e-01 1.21e+00 1.61e+01 angle pdb=" C SER H 92 " pdb=" CA SER H 92 " pdb=" CB SER H 92 " ideal model delta sigma weight residual 116.63 112.04 4.59 1.16e+00 7.43e-01 1.56e+01 angle pdb=" C SER D 92 " pdb=" N CYS D 93 " pdb=" CA CYS D 93 " ideal model delta sigma weight residual 121.54 114.03 7.51 1.91e+00 2.74e-01 1.55e+01 ... (remaining 41637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 16631 17.64 - 35.27: 1735 35.27 - 52.91: 410 52.91 - 70.54: 70 70.54 - 88.18: 34 Dihedral angle restraints: 18880 sinusoidal: 7985 harmonic: 10895 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 175.26 -82.26 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.10 -80.90 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -163.45 77.45 1 1.00e+01 1.00e-02 7.51e+01 ... (remaining 18877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 4923 0.169 - 0.338: 9 0.338 - 0.506: 1 0.506 - 0.675: 0 0.675 - 0.844: 1 Chirality restraints: 4934 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.78e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.37e+00 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 -2.10 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 4931 not shown) Planarity restraints: 5338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 81 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C ASN C 81 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN C 81 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO C 82 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 92 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C SER D 92 " -0.041 2.00e-02 2.50e+03 pdb=" O SER D 92 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS D 93 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 614 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ASP C 614 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP C 614 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL C 615 " 0.012 2.00e-02 2.50e+03 ... (remaining 5335 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2730 2.74 - 3.28: 28994 3.28 - 3.82: 47777 3.82 - 4.36: 53254 4.36 - 4.90: 95296 Nonbonded interactions: 228051 Sorted by model distance: nonbonded pdb=" N GLU B 583 " pdb=" OE1 GLU B 583 " model vdw 2.203 3.120 nonbonded pdb=" OD1 ASP A 663 " pdb=" OG SER A 673 " model vdw 2.211 3.040 nonbonded pdb=" O PHE A 329 " pdb=" NE2 GLN A 580 " model vdw 2.224 3.120 nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.226 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.227 3.040 ... (remaining 228046 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 518 or (resid 519 through 520 and (name N or na \ me CA or name C or name O or name CB )) or resid 521 through 527 or (resid 528 a \ nd (name N or name CA or name C or name O or name CB )) or resid 529 through 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 1147 or resid 1301 through 1309)) selection = (chain 'B' and (resid 15 through 527 or (resid 528 and (name N or name CA or nam \ e C or name O or name CB )) or resid 529 through 555 or (resid 556 and (name N o \ r name CA or name C or name O or name CB )) or resid 557 or (resid 558 through 5 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 560 through \ 785 or (resid 786 and (name N or name CA or name C or name O or name CB )) or r \ esid 787 through 827 or (resid 854 and (name N or name CA or name C or name O or \ name CB )) or resid 855 through 903 or (resid 904 and (name N or name CA or nam \ e 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)) selection = (chain 'C' and (resid 15 through 557 or (resid 558 through 559 and (name N or na \ me CA or name C or name O or name CB )) or resid 560 through 827 or resid 854 th \ rough 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 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' } 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: 190.160 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: 0.050 Extract box with map and model: 1.360 Check model and map are aligned: 0.270 Set scattering table: 0.290 Process input model: 78.190 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.240 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 275.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 0.045 30686 Z= 0.183 Angle : 0.620 14.803 41911 Z= 0.314 Chirality : 0.047 0.844 4934 Planarity : 0.003 0.048 5294 Dihedral : 14.799 88.180 11753 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.75 % Favored : 95.15 % Rotamer: Outliers : 0.12 % Allowed : 18.48 % Favored : 81.40 % 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: -0.28 (0.14), residues: 3709 helix: 2.02 (0.22), residues: 643 sheet: 0.51 (0.17), residues: 963 loop : -1.30 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 353 HIS 0.003 0.001 HIS E 55 PHE 0.016 0.001 PHE D 91 TYR 0.015 0.001 TYR B1067 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 44) link_NAG-ASN : angle 2.77220 ( 132) link_BETA1-4 : bond 0.00374 ( 17) link_BETA1-4 : angle 1.44496 ( 51) hydrogen bonds : bond 0.15027 ( 1103) hydrogen bonds : angle 6.80514 ( 3042) SS BOND : bond 0.00366 ( 43) SS BOND : angle 1.12840 ( 86) covalent geometry : bond 0.00366 (30582) covalent geometry : angle 0.59751 (41642) *********************** 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 144 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 3.322 Fit side-chains REVERT: E 33 MET cc_start: 0.6239 (tpt) cc_final: 0.6013 (tpt) REVERT: H 74 MET cc_start: 0.0934 (pmm) cc_final: -0.1723 (ttp) outliers start: 4 outliers final: 2 residues processed: 142 average time/residue: 0.3718 time to fit residues: 91.1031 Evaluate side-chains 116 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 40.0000 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 292 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 0.0070 chunk 338 optimal weight: 4.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 804 GLN B 935 GLN C 901 GLN C1106 GLN H 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.131497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076062 restraints weight = 86356.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077717 restraints weight = 37103.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.076421 restraints weight = 24280.422| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30686 Z= 0.161 Angle : 0.575 13.439 41911 Z= 0.290 Chirality : 0.045 0.544 4934 Planarity : 0.004 0.046 5294 Dihedral : 6.755 59.650 5315 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 2.90 % Allowed : 17.26 % Favored : 79.84 % 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: -0.19 (0.14), residues: 3709 helix: 2.15 (0.21), residues: 654 sheet: 0.54 (0.17), residues: 944 loop : -1.25 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.003 0.001 HIS C1064 PHE 0.017 0.001 PHE B 157 TYR 0.017 0.001 TYR A1067 ARG 0.004 0.000 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 44) link_NAG-ASN : angle 2.66127 ( 132) link_BETA1-4 : bond 0.00403 ( 17) link_BETA1-4 : angle 1.15971 ( 51) hydrogen bonds : bond 0.04617 ( 1103) hydrogen bonds : angle 5.55473 ( 3042) SS BOND : bond 0.00367 ( 43) SS BOND : angle 1.19042 ( 86) covalent geometry : bond 0.00369 (30582) covalent geometry : angle 0.55300 (41642) *********************** 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 221 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 128 time to evaluate : 4.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4211 (tmm) cc_final: 0.3532 (tmm) REVERT: B 781 VAL cc_start: 0.9038 (p) cc_final: 0.8838 (p) REVERT: G 33 MET cc_start: 0.1068 (mmm) cc_final: 0.0762 (mmt) outliers start: 93 outliers final: 55 residues processed: 209 average time/residue: 0.4848 time to fit residues: 178.5628 Evaluate side-chains 176 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 4.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 154 optimal weight: 0.9980 chunk 223 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 333 optimal weight: 0.4980 chunk 368 optimal weight: 40.0000 chunk 167 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 242 optimal weight: 20.0000 chunk 197 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 955 ASN H 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.130705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.075435 restraints weight = 88022.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.076719 restraints weight = 37228.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078087 restraints weight = 22907.734| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30686 Z= 0.153 Angle : 0.554 13.231 41911 Z= 0.278 Chirality : 0.044 0.501 4934 Planarity : 0.003 0.045 5294 Dihedral : 6.125 59.703 5315 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.23 % Rotamer: Outliers : 3.30 % Allowed : 17.58 % Favored : 79.12 % 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: -0.17 (0.14), residues: 3709 helix: 2.18 (0.21), residues: 654 sheet: 0.51 (0.17), residues: 974 loop : -1.23 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.002 0.001 HIS B1088 PHE 0.019 0.001 PHE E 106 TYR 0.016 0.001 TYR C1067 ARG 0.004 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 44) link_NAG-ASN : angle 2.64990 ( 132) link_BETA1-4 : bond 0.00322 ( 17) link_BETA1-4 : angle 1.18294 ( 51) hydrogen bonds : bond 0.04392 ( 1103) hydrogen bonds : angle 5.35459 ( 3042) SS BOND : bond 0.00383 ( 43) SS BOND : angle 1.41185 ( 86) covalent geometry : bond 0.00353 (30582) covalent geometry : angle 0.52981 (41642) *********************** 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 236 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 130 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4122 (tmm) cc_final: 0.3727 (tmm) REVERT: B 726 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9031 (tp) REVERT: B 727 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9323 (pp) REVERT: B 748 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: I 33 MET cc_start: 0.3768 (mmp) cc_final: 0.2765 (ppp) outliers start: 106 outliers final: 69 residues processed: 223 average time/residue: 0.4226 time to fit residues: 166.6053 Evaluate side-chains 195 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 123 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 14 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 313 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 362 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 296 optimal weight: 0.0770 chunk 57 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.130459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.075590 restraints weight = 87710.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.077488 restraints weight = 36598.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.078404 restraints weight = 22672.761| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30686 Z= 0.138 Angle : 0.538 13.132 41911 Z= 0.270 Chirality : 0.044 0.485 4934 Planarity : 0.003 0.044 5294 Dihedral : 5.680 59.725 5315 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.91 % Favored : 95.07 % Rotamer: Outliers : 3.30 % Allowed : 18.14 % Favored : 78.56 % 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: -0.12 (0.14), residues: 3709 helix: 2.22 (0.21), residues: 653 sheet: 0.61 (0.17), residues: 975 loop : -1.25 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 353 HIS 0.003 0.000 HIS B1088 PHE 0.016 0.001 PHE A 106 TYR 0.015 0.001 TYR A1067 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 44) link_NAG-ASN : angle 2.61268 ( 132) link_BETA1-4 : bond 0.00326 ( 17) link_BETA1-4 : angle 1.17791 ( 51) hydrogen bonds : bond 0.04183 ( 1103) hydrogen bonds : angle 5.19944 ( 3042) SS BOND : bond 0.00332 ( 43) SS BOND : angle 1.18396 ( 86) covalent geometry : bond 0.00318 (30582) covalent geometry : angle 0.51474 (41642) *********************** 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 234 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 128 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8807 (mp) cc_final: 0.8582 (mt) REVERT: A 505 TYR cc_start: 0.6370 (m-80) cc_final: 0.6152 (m-80) REVERT: B 726 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8999 (tp) REVERT: B 727 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9336 (pp) REVERT: I 33 MET cc_start: 0.3557 (mmp) cc_final: 0.2753 (ppp) outliers start: 106 outliers final: 77 residues processed: 223 average time/residue: 0.3488 time to fit residues: 136.7026 Evaluate side-chains 197 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 118 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 183 optimal weight: 0.7980 chunk 281 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 265 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 137 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 493 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.130818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075085 restraints weight = 86222.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.075885 restraints weight = 37650.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.076876 restraints weight = 23983.221| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30686 Z= 0.181 Angle : 0.561 13.692 41911 Z= 0.281 Chirality : 0.045 0.499 4934 Planarity : 0.003 0.044 5294 Dihedral : 5.521 59.842 5315 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.83 % Allowed : 18.64 % Favored : 77.53 % 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: -0.20 (0.14), residues: 3709 helix: 2.11 (0.21), residues: 661 sheet: 0.43 (0.17), residues: 974 loop : -1.22 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.003 0.001 HIS B1088 PHE 0.015 0.001 PHE B 157 TYR 0.016 0.001 TYR C1067 ARG 0.007 0.000 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 44) link_NAG-ASN : angle 2.65411 ( 132) link_BETA1-4 : bond 0.00310 ( 17) link_BETA1-4 : angle 1.19770 ( 51) hydrogen bonds : bond 0.04328 ( 1103) hydrogen bonds : angle 5.19341 ( 3042) SS BOND : bond 0.00373 ( 43) SS BOND : angle 1.24990 ( 86) covalent geometry : bond 0.00420 (30582) covalent geometry : angle 0.53750 (41642) *********************** 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 245 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 122 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5091 (tmm) cc_final: 0.4568 (tmm) REVERT: B 214 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5687 (tpt90) REVERT: B 725 GLU cc_start: 0.7714 (tt0) cc_final: 0.7403 (tt0) REVERT: B 726 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9026 (tp) REVERT: B 727 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9376 (pp) REVERT: H 74 MET cc_start: 0.1473 (pmm) cc_final: 0.1179 (pmm) REVERT: I 33 MET cc_start: 0.3512 (mmp) cc_final: 0.2811 (ppp) outliers start: 123 outliers final: 92 residues processed: 236 average time/residue: 0.3603 time to fit residues: 149.3756 Evaluate side-chains 214 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 119 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 116 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 341 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 252 optimal weight: 0.0970 chunk 289 optimal weight: 4.9990 chunk 363 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 365 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 777 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.130246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.076306 restraints weight = 88848.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076730 restraints weight = 37200.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.078014 restraints weight = 22943.485| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30686 Z= 0.156 Angle : 0.547 13.481 41911 Z= 0.274 Chirality : 0.044 0.483 4934 Planarity : 0.003 0.044 5294 Dihedral : 5.345 59.799 5315 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.93 % Allowed : 18.95 % Favored : 77.13 % 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: -0.18 (0.14), residues: 3709 helix: 2.14 (0.21), residues: 661 sheet: 0.51 (0.17), residues: 965 loop : -1.24 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.002 0.000 HIS A1064 PHE 0.023 0.001 PHE C 855 TYR 0.015 0.001 TYR C1067 ARG 0.009 0.000 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 44) link_NAG-ASN : angle 2.62784 ( 132) link_BETA1-4 : bond 0.00338 ( 17) link_BETA1-4 : angle 1.20818 ( 51) hydrogen bonds : bond 0.04186 ( 1103) hydrogen bonds : angle 5.11776 ( 3042) SS BOND : bond 0.00360 ( 43) SS BOND : angle 1.20745 ( 86) covalent geometry : bond 0.00361 (30582) covalent geometry : angle 0.52383 (41642) *********************** 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 252 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 126 time to evaluate : 3.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4139 (tmm) cc_final: 0.3452 (tmm) REVERT: A 271 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: A 1029 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.7869 (ttp) REVERT: B 725 GLU cc_start: 0.7600 (tt0) cc_final: 0.7365 (tt0) REVERT: B 726 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9008 (tp) REVERT: B 727 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9377 (pp) REVERT: C 614 ASP cc_start: 0.7842 (t0) cc_final: 0.7359 (t0) REVERT: H 74 MET cc_start: 0.0960 (pmm) cc_final: 0.0697 (pmm) REVERT: I 33 MET cc_start: 0.3466 (mmp) cc_final: 0.2881 (ppp) outliers start: 126 outliers final: 97 residues processed: 241 average time/residue: 0.5686 time to fit residues: 246.1213 Evaluate side-chains 223 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 122 time to evaluate : 5.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 250 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 224 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 310 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 17 optimal weight: 0.2980 chunk 214 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.130570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076256 restraints weight = 88878.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077643 restraints weight = 37894.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078951 restraints weight = 23211.750| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30686 Z= 0.131 Angle : 0.537 13.379 41911 Z= 0.267 Chirality : 0.044 0.475 4934 Planarity : 0.003 0.044 5294 Dihedral : 5.155 59.135 5315 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.68 % Allowed : 19.26 % Favored : 77.06 % 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: -0.12 (0.14), residues: 3709 helix: 2.21 (0.21), residues: 661 sheet: 0.48 (0.17), residues: 982 loop : -1.18 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.002 0.000 HIS B1088 PHE 0.015 0.001 PHE B 157 TYR 0.015 0.001 TYR A1067 ARG 0.008 0.000 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 44) link_NAG-ASN : angle 2.61161 ( 132) link_BETA1-4 : bond 0.00335 ( 17) link_BETA1-4 : angle 1.20513 ( 51) hydrogen bonds : bond 0.04023 ( 1103) hydrogen bonds : angle 5.02986 ( 3042) SS BOND : bond 0.00332 ( 43) SS BOND : angle 1.12841 ( 86) covalent geometry : bond 0.00302 (30582) covalent geometry : angle 0.51370 (41642) *********************** 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 246 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 128 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4074 (tmm) cc_final: 0.3442 (tmm) REVERT: A 271 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8348 (mp10) REVERT: A 1029 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.7826 (ttp) REVERT: B 726 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8992 (tp) REVERT: B 727 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9369 (pp) REVERT: C 614 ASP cc_start: 0.7834 (t0) cc_final: 0.7381 (t0) REVERT: H 74 MET cc_start: 0.1041 (pmm) cc_final: 0.0607 (pmm) REVERT: I 33 MET cc_start: 0.3629 (mmp) cc_final: 0.2980 (ppp) outliers start: 118 outliers final: 94 residues processed: 235 average time/residue: 0.3709 time to fit residues: 153.5232 Evaluate side-chains 216 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 118 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 221 optimal weight: 0.4980 chunk 332 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 328 optimal weight: 3.9990 chunk 334 optimal weight: 0.1980 chunk 258 optimal weight: 6.9990 chunk 172 optimal weight: 0.0980 chunk 137 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.130681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075985 restraints weight = 89031.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077702 restraints weight = 37734.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078513 restraints weight = 23042.882| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30686 Z= 0.129 Angle : 0.538 12.162 41911 Z= 0.268 Chirality : 0.044 0.661 4934 Planarity : 0.003 0.043 5294 Dihedral : 5.025 57.702 5315 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.52 % Allowed : 19.63 % Favored : 76.85 % 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: -0.13 (0.14), residues: 3709 helix: 2.18 (0.21), residues: 661 sheet: 0.39 (0.17), residues: 1005 loop : -1.15 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 353 HIS 0.002 0.000 HIS B1088 PHE 0.018 0.001 PHE A 347 TYR 0.015 0.001 TYR A1067 ARG 0.008 0.000 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 44) link_NAG-ASN : angle 2.59281 ( 132) link_BETA1-4 : bond 0.00338 ( 17) link_BETA1-4 : angle 1.22123 ( 51) hydrogen bonds : bond 0.03954 ( 1103) hydrogen bonds : angle 4.98325 ( 3042) SS BOND : bond 0.00330 ( 43) SS BOND : angle 1.09728 ( 86) covalent geometry : bond 0.00298 (30582) covalent geometry : angle 0.51558 (41642) *********************** 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 235 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 122 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4200 (tmm) cc_final: 0.3566 (tmm) REVERT: A 271 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8344 (mp10) REVERT: A 1029 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.7803 (ttp) REVERT: B 726 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8986 (tp) REVERT: B 727 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9358 (pp) REVERT: C 614 ASP cc_start: 0.7844 (t0) cc_final: 0.7402 (t0) REVERT: H 74 MET cc_start: 0.1359 (pmm) cc_final: 0.1093 (pmm) REVERT: I 33 MET cc_start: 0.3741 (mmp) cc_final: 0.3107 (ppp) outliers start: 113 outliers final: 100 residues processed: 223 average time/residue: 0.3636 time to fit residues: 144.0625 Evaluate side-chains 224 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 120 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 237 optimal weight: 6.9990 chunk 304 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 334 optimal weight: 0.7980 chunk 284 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 274 optimal weight: 0.9980 chunk 249 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.131773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.078050 restraints weight = 88325.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.079541 restraints weight = 36867.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080851 restraints weight = 22377.814| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30686 Z= 0.106 Angle : 0.525 11.646 41911 Z= 0.261 Chirality : 0.044 0.593 4934 Planarity : 0.003 0.043 5294 Dihedral : 4.837 55.014 5315 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.05 % Allowed : 20.19 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.21 (0.21), residues: 667 sheet: 0.40 (0.17), residues: 1012 loop : -1.10 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 353 HIS 0.002 0.000 HIS B1088 PHE 0.014 0.001 PHE B 157 TYR 0.016 0.001 TYR A1067 ARG 0.008 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 44) link_NAG-ASN : angle 2.54021 ( 132) link_BETA1-4 : bond 0.00359 ( 17) link_BETA1-4 : angle 1.20871 ( 51) hydrogen bonds : bond 0.03756 ( 1103) hydrogen bonds : angle 4.88848 ( 3042) SS BOND : bond 0.00312 ( 43) SS BOND : angle 1.00216 ( 86) covalent geometry : bond 0.00241 (30582) covalent geometry : angle 0.50272 (41642) *********************** 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 212 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 114 time to evaluate : 5.434 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.4201 (tmm) cc_final: 0.3580 (tmm) REVERT: A 271 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8349 (mp10) REVERT: A 1029 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.7777 (ttp) REVERT: B 726 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9022 (tp) REVERT: B 727 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9341 (pp) REVERT: B 988 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8217 (tm-30) REVERT: C 614 ASP cc_start: 0.7762 (t0) cc_final: 0.7327 (t0) REVERT: I 33 MET cc_start: 0.3759 (mmp) cc_final: 0.2998 (ppp) outliers start: 98 outliers final: 87 residues processed: 201 average time/residue: 0.5012 time to fit residues: 184.3560 Evaluate side-chains 203 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 112 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 68 optimal weight: 0.8980 chunk 352 optimal weight: 0.7980 chunk 345 optimal weight: 0.0970 chunk 114 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 278 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 292 optimal weight: 0.7980 chunk 324 optimal weight: 20.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1088 HIS D 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.131644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.077978 restraints weight = 88318.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079325 restraints weight = 36449.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.080693 restraints weight = 22062.276| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30686 Z= 0.096 Angle : 0.522 10.788 41911 Z= 0.260 Chirality : 0.044 0.566 4934 Planarity : 0.003 0.044 5294 Dihedral : 4.670 51.480 5315 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.93 % Allowed : 20.38 % Favored : 76.69 % 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: 2.27 (0.22), residues: 661 sheet: 0.42 (0.17), residues: 1014 loop : -1.08 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 353 HIS 0.002 0.000 HIS B1088 PHE 0.014 0.001 PHE B 157 TYR 0.016 0.001 TYR A1067 ARG 0.009 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 44) link_NAG-ASN : angle 2.49541 ( 132) link_BETA1-4 : bond 0.00376 ( 17) link_BETA1-4 : angle 1.22003 ( 51) hydrogen bonds : bond 0.03604 ( 1103) hydrogen bonds : angle 4.82082 ( 3042) SS BOND : bond 0.00305 ( 43) SS BOND : angle 0.94207 ( 86) covalent geometry : bond 0.00215 (30582) covalent geometry : angle 0.50097 (41642) ********************** 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 207 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 113 time to evaluate : 3.275 Fit side-chains REVERT: A 153 MET cc_start: 0.4272 (tmm) cc_final: 0.3659 (tmm) REVERT: A 271 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8340 (mp10) REVERT: A 1029 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.7671 (ttp) REVERT: B 727 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9328 (pp) REVERT: B 988 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 614 ASP cc_start: 0.7753 (t0) cc_final: 0.7358 (t0) REVERT: I 33 MET cc_start: 0.3728 (mmp) cc_final: 0.2916 (ppp) outliers start: 94 outliers final: 80 residues processed: 198 average time/residue: 0.3469 time to fit residues: 121.3833 Evaluate side-chains 194 residues out of total 3255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 111 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 119 optimal weight: 5.9990 chunk 163 optimal weight: 0.0670 chunk 293 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 336 optimal weight: 30.0000 chunk 350 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 340 optimal weight: 8.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.130551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.076814 restraints weight = 88789.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077570 restraints weight = 38332.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078899 restraints weight = 23593.277| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30686 Z= 0.187 Angle : 0.570 11.537 41911 Z= 0.284 Chirality : 0.045 0.604 4934 Planarity : 0.003 0.044 5294 Dihedral : 4.808 48.848 5315 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.18 % Allowed : 20.04 % Favored : 76.78 % 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: -0.13 (0.14), residues: 3709 helix: 2.14 (0.21), residues: 667 sheet: 0.35 (0.17), residues: 1016 loop : -1.12 (0.14), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 353 HIS 0.002 0.001 HIS B1088 PHE 0.015 0.001 PHE B 157 TYR 0.015 0.001 TYR C1067 ARG 0.009 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 44) link_NAG-ASN : angle 2.57123 ( 132) link_BETA1-4 : bond 0.00302 ( 17) link_BETA1-4 : angle 1.21140 ( 51) hydrogen bonds : bond 0.04137 ( 1103) hydrogen bonds : angle 4.98032 ( 3042) SS BOND : bond 0.00356 ( 43) SS BOND : angle 1.32215 ( 86) covalent geometry : bond 0.00436 (30582) covalent geometry : angle 0.54785 (41642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16461.77 seconds wall clock time: 295 minutes 42.21 seconds (17742.21 seconds total)