Starting phenix.real_space_refine on Thu Jun 26 08:52:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws0_32739/06_2025/7ws0_32739_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws0_32739/06_2025/7ws0_32739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws0_32739/06_2025/7ws0_32739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws0_32739/06_2025/7ws0_32739.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws0_32739/06_2025/7ws0_32739_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws0_32739/06_2025/7ws0_32739_neut.cif" } resolution = 3.2 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= 0.047 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 135 5.16 5 C 19326 2.51 5 N 4978 2.21 5 O 6001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 2.74s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30440 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8071 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 7 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 8056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8056 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 8061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8061 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 52, 'TRANS': 986} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 20.65, per 1000 atoms: 0.68 Number of scatterers: 30440 At special positions: 0 Unit cell: (136.12, 150.06, 211.56, 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 135 16.00 O 6001 8.00 N 4978 7.00 C 19326 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.02 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 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 7.64 Conformation dependent library (CDL) restraints added in 3.9 seconds 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7124 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 74 sheets defined 21.6% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 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 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.536A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.718A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.820A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.581A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.614A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.952A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.732A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.137A 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: 3.692A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.093A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.492A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.062A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.747A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.019A 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 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.727A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.758A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.564A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.949A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.601A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.876A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.313A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.820A 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: 3.871A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.477A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.828A 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 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.396A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.734A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.794A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) 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 760 through 783 removed outlier: 3.886A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.843A 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 removed outlier: 3.586A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.913A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.816A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.508A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.774A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.551A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.155A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.064A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.987A pdb=" N ASP E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.548A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.819A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.987A pdb=" N ASP G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.548A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.819A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.987A pdb=" N ASP I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.547A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.819A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.504A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.215A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.532A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 135 removed outlier: 3.516A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.552A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.941A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.081A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.821A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.688A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.130A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.693A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.566A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.474A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.806A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.876A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.436A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 132 through 142 removed outlier: 4.312A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.178A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.242A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.481A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.834A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.326A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.495A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.237A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.589A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 5.851A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.913A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.142A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.293A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.240A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.140A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.119A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.468A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 4.694A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.710A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AG2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.921A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.743A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG5, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR E 112 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR E 94 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.708A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AG9, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.923A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.744A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AH3, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR G 112 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR G 94 " --> pdb=" O THR G 117 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.711A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AH7, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.923A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR H 98 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.745A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AI1, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.677A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR I 112 " --> pdb=" O LYS I 98 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.677A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR I 94 " --> pdb=" O THR I 117 " (cutoff:3.500A) 1135 hydrogen bonds defined for protein. 3057 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: 18.57 Time building geometry restraints manager: 9.10 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: 9690 1.35 - 1.47: 7942 1.47 - 1.59: 13311 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 31117 Sorted by residual: bond pdb=" N ARG H 18 " pdb=" CA ARG H 18 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.20e-02 6.94e+03 8.22e+00 bond pdb=" N ILE A 210 " pdb=" CA ILE A 210 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.21e+00 bond pdb=" N TYR B 449 " pdb=" CA TYR B 449 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 7.98e+00 bond pdb=" N ASP I 31 " pdb=" CA ASP I 31 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.25e-02 6.40e+03 7.64e+00 bond pdb=" N ASP G 31 " pdb=" CA ASP G 31 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.25e-02 6.40e+03 7.64e+00 ... (remaining 31112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 41581 2.05 - 4.09: 718 4.09 - 6.14: 54 6.14 - 8.18: 4 8.18 - 10.23: 1 Bond angle restraints: 42358 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.72 -4.02 1.22e+00 6.72e-01 1.08e+01 angle pdb=" CA ASN B 360 " pdb=" C ASN B 360 " pdb=" O ASN B 360 " ideal model delta sigma weight residual 122.14 118.07 4.07 1.24e+00 6.50e-01 1.08e+01 angle pdb=" CA SER B 359 " pdb=" C SER B 359 " pdb=" O SER B 359 " ideal model delta sigma weight residual 121.45 117.96 3.49 1.07e+00 8.73e-01 1.06e+01 angle pdb=" CB LYS C 814 " pdb=" CG LYS C 814 " pdb=" CD LYS C 814 " ideal model delta sigma weight residual 111.30 118.76 -7.46 2.30e+00 1.89e-01 1.05e+01 angle pdb=" C GLY B 744 " pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 ... (remaining 42353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 17649 18.08 - 36.15: 1335 36.15 - 54.23: 261 54.23 - 72.30: 50 72.30 - 90.38: 25 Dihedral angle restraints: 19320 sinusoidal: 8239 harmonic: 11081 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 -176.62 -90.38 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.34 -88.66 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -171.65 85.65 1 1.00e+01 1.00e-02 8.87e+01 ... (remaining 19317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4968 0.150 - 0.300: 12 0.300 - 0.451: 1 0.451 - 0.601: 1 0.601 - 0.751: 2 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.26e+00 ... (remaining 4981 not shown) Planarity restraints: 5446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO B 987 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO B 561 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 425 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 426 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 426 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 426 " 0.028 5.00e-02 4.00e+02 ... (remaining 5443 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4361 2.76 - 3.29: 27610 3.29 - 3.83: 47386 3.83 - 4.36: 54804 4.36 - 4.90: 98931 Nonbonded interactions: 233092 Sorted by model distance: nonbonded pdb=" OE1 GLU A 819 " pdb=" OG SER A1055 " model vdw 2.225 3.040 nonbonded pdb=" OE1 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.252 3.040 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.258 3.120 nonbonded pdb=" NH1 ARG F 61 " pdb=" OD2 ASP F 82 " model vdw 2.258 3.120 ... (remaining 233087 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 108 or (resid 109 through 110 and (name N or na \ me CA or name C or name O or name CB )) or resid 111 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 or (resid 5 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 557 through \ 827 or resid 854 through 984 or (resid 985 and (name N or name CA or name C or \ name O or name CB )) or resid 986 through 1044 or (resid 1045 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1046 through 1147 or resid 1301 \ through 1310)) selection = (chain 'B' and (resid 15 through 555 or (resid 556 and (name N or name CA or nam \ e C or name O or name CB )) or resid 557 or (resid 558 through 559 and (name N o \ r name CA or name C or name O or name CB )) or resid 560 through 785 or (resid 7 \ 86 and (name N or name CA or name C or name O or name CB )) or resid 787 through \ 827 or (resid 854 and (name N or name CA or name C or name O or name CB )) or r \ esid 855 through 903 or (resid 904 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ ) \ ) or resid 905 through 1044 or (resid 1045 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1046 through 1147 or resid 1301 through 1310)) selection = (chain 'C' and (resid 15 through 108 or (resid 109 through 110 and (name N or na \ me CA or name C or name O or name CB )) or resid 111 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 through 557 \ or (resid 558 through 559 and (name N or name CA or name C or name O or name CB \ )) or resid 560 through 827 or resid 854 through 903 or (resid 904 and (name N \ or name CA 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 984 or (resid 985 and (n \ ame N or name CA or name C or name O or name CB )) or resid 986 through 1147 or \ resid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.390 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: 0.070 Extract box with map and model: 1.170 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 79.340 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.230 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 0.043 31226 Z= 0.213 Angle : 0.645 14.334 42642 Z= 0.340 Chirality : 0.048 0.751 4984 Planarity : 0.004 0.062 5398 Dihedral : 13.183 89.343 12067 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.14), residues: 3757 helix: 1.01 (0.21), residues: 672 sheet: -0.35 (0.17), residues: 1016 loop : -1.29 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.003 0.001 HIS B1064 PHE 0.022 0.001 PHE B 906 TYR 0.025 0.001 TYR C 453 ARG 0.005 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 48) link_NAG-ASN : angle 2.91160 ( 144) link_BETA1-4 : bond 0.00442 ( 18) link_BETA1-4 : angle 1.54245 ( 54) hydrogen bonds : bond 0.23455 ( 1094) hydrogen bonds : angle 8.57237 ( 3057) SS BOND : bond 0.00355 ( 43) SS BOND : angle 1.15398 ( 86) covalent geometry : bond 0.00393 (31117) covalent geometry : angle 0.61971 (42358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8352 (p) cc_final: 0.8145 (p) REVERT: A 242 LEU cc_start: 0.6996 (mt) cc_final: 0.6715 (mt) REVERT: C 814 LYS cc_start: 0.6977 (mmmt) cc_final: 0.6543 (ptpp) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.4244 time to fit residues: 314.3241 Evaluate side-chains 298 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 114 optimal weight: 0.0870 chunk 179 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 341 optimal weight: 0.0770 overall best weight: 1.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 580 GLN A 955 ASN A1002 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 422 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 774 GLN C 804 GLN C 935 GLN D 34 ASN D 89 GLN E 54 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 37 GLN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.129839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.084648 restraints weight = 56498.963| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.62 r_work: 0.3017 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31226 Z= 0.172 Angle : 0.644 13.821 42642 Z= 0.326 Chirality : 0.048 0.524 4984 Planarity : 0.005 0.065 5398 Dihedral : 6.357 59.435 5478 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.26 % Allowed : 7.88 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.13), residues: 3757 helix: 1.52 (0.22), residues: 653 sheet: -0.22 (0.16), residues: 1015 loop : -1.34 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 113 HIS 0.004 0.001 HIS B1048 PHE 0.021 0.002 PHE C 168 TYR 0.028 0.002 TYR A1067 ARG 0.008 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 48) link_NAG-ASN : angle 2.71508 ( 144) link_BETA1-4 : bond 0.00467 ( 18) link_BETA1-4 : angle 1.11544 ( 54) hydrogen bonds : bond 0.04932 ( 1094) hydrogen bonds : angle 5.92135 ( 3057) SS BOND : bond 0.00741 ( 43) SS BOND : angle 1.33315 ( 86) covalent geometry : bond 0.00403 (31117) covalent geometry : angle 0.62217 (42358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 334 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8102 (mt) cc_final: 0.7633 (mt) REVERT: A 346 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.8111 (mtm-85) REVERT: C 462 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8362 (pttt) REVERT: C 505 TYR cc_start: 0.7598 (t80) cc_final: 0.7372 (t80) REVERT: C 902 MET cc_start: 0.9279 (mmm) cc_final: 0.8834 (mmt) REVERT: C 988 GLU cc_start: 0.8535 (mp0) cc_final: 0.8139 (mp0) REVERT: G 71 SER cc_start: 0.7934 (t) cc_final: 0.7652 (p) REVERT: H 24 ARG cc_start: 0.6650 (ttp80) cc_final: 0.5992 (mtp-110) REVERT: H 83 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7142 (p90) REVERT: I 68 PHE cc_start: 0.7279 (m-10) cc_final: 0.6976 (m-10) outliers start: 41 outliers final: 29 residues processed: 357 average time/residue: 0.4126 time to fit residues: 240.7740 Evaluate side-chains 323 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 3.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 123 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 365 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 321 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 262 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 532 ASN A 955 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 675 GLN C 804 GLN C 935 GLN F 6 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.129877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084955 restraints weight = 56736.303| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.63 r_work: 0.3025 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31226 Z= 0.125 Angle : 0.573 13.726 42642 Z= 0.287 Chirality : 0.045 0.466 4984 Planarity : 0.004 0.061 5398 Dihedral : 5.610 59.615 5478 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.17 % Allowed : 10.59 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (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: -0.57 (0.14), residues: 3757 helix: 1.82 (0.22), residues: 652 sheet: -0.04 (0.16), residues: 1018 loop : -1.31 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 53 HIS 0.002 0.001 HIS B1064 PHE 0.024 0.001 PHE G 27 TYR 0.020 0.001 TYR A1067 ARG 0.012 0.000 ARG F 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 48) link_NAG-ASN : angle 2.61259 ( 144) link_BETA1-4 : bond 0.00417 ( 18) link_BETA1-4 : angle 1.23307 ( 54) hydrogen bonds : bond 0.04632 ( 1094) hydrogen bonds : angle 5.46195 ( 3057) SS BOND : bond 0.00547 ( 43) SS BOND : angle 1.23526 ( 86) covalent geometry : bond 0.00288 (31117) covalent geometry : angle 0.55007 (42358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 317 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8049 (mt) cc_final: 0.7593 (mt) REVERT: A 346 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8045 (mtm-85) REVERT: A 449 TYR cc_start: 0.8584 (m-80) cc_final: 0.8141 (m-80) REVERT: A 745 ASP cc_start: 0.7867 (t0) cc_final: 0.7456 (t0) REVERT: A 979 ASP cc_start: 0.8260 (t0) cc_final: 0.8026 (t0) REVERT: B 493 GLN cc_start: 0.7225 (mp10) cc_final: 0.6984 (mp-120) REVERT: B 661 GLU cc_start: 0.8847 (pt0) cc_final: 0.8645 (tp30) REVERT: B 804 GLN cc_start: 0.8876 (mm110) cc_final: 0.8667 (mm110) REVERT: C 462 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8385 (pttt) REVERT: C 493 GLN cc_start: 0.5150 (mp10) cc_final: 0.4847 (mp10) REVERT: C 505 TYR cc_start: 0.7672 (t80) cc_final: 0.7284 (t80) REVERT: C 574 ASP cc_start: 0.8146 (t70) cc_final: 0.7824 (t0) REVERT: C 675 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6662 (tm130) REVERT: C 814 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7568 (mmmt) REVERT: C 902 MET cc_start: 0.9276 (mmm) cc_final: 0.8809 (mmt) REVERT: C 988 GLU cc_start: 0.8554 (mp0) cc_final: 0.8106 (mp0) REVERT: E 68 PHE cc_start: 0.5817 (m-10) cc_final: 0.5553 (m-80) REVERT: E 100 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7288 (mtt180) REVERT: F 4 MET cc_start: 0.5803 (OUTLIER) cc_final: 0.5563 (mmm) REVERT: F 11 LEU cc_start: 0.8365 (mp) cc_final: 0.7816 (tp) REVERT: H 21 ILE cc_start: 0.7467 (mm) cc_final: 0.7247 (mp) REVERT: H 82 ASP cc_start: 0.7464 (m-30) cc_final: 0.7100 (m-30) REVERT: H 83 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7124 (p90) REVERT: I 46 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6969 (mm-30) REVERT: I 68 PHE cc_start: 0.7434 (m-10) cc_final: 0.7120 (m-80) REVERT: I 105 LEU cc_start: 0.7617 (mp) cc_final: 0.7408 (tt) outliers start: 38 outliers final: 24 residues processed: 337 average time/residue: 0.4048 time to fit residues: 223.1808 Evaluate side-chains 325 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 64 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 2 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 366 optimal weight: 0.6980 chunk 292 optimal weight: 2.9990 chunk 320 optimal weight: 8.9990 chunk 180 optimal weight: 0.6980 chunk 360 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** B 115 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.128317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.083443 restraints weight = 56771.251| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.61 r_work: 0.2996 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31226 Z= 0.147 Angle : 0.576 13.978 42642 Z= 0.288 Chirality : 0.045 0.479 4984 Planarity : 0.004 0.062 5398 Dihedral : 5.299 59.120 5478 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.63 % Allowed : 11.88 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3757 helix: 1.89 (0.22), residues: 653 sheet: 0.03 (0.16), residues: 1057 loop : -1.27 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 53 HIS 0.003 0.001 HIS B1088 PHE 0.020 0.001 PHE A 106 TYR 0.020 0.001 TYR A1067 ARG 0.019 0.000 ARG I 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 48) link_NAG-ASN : angle 2.63137 ( 144) link_BETA1-4 : bond 0.00325 ( 18) link_BETA1-4 : angle 1.16829 ( 54) hydrogen bonds : bond 0.04643 ( 1094) hydrogen bonds : angle 5.25789 ( 3057) SS BOND : bond 0.00665 ( 43) SS BOND : angle 1.29955 ( 86) covalent geometry : bond 0.00352 (31117) covalent geometry : angle 0.55273 (42358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 322 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ARG cc_start: 0.8238 (tpm170) cc_final: 0.7798 (tpp-160) REVERT: A 745 ASP cc_start: 0.7829 (t0) cc_final: 0.7362 (t0) REVERT: A 760 CYS cc_start: 0.9106 (m) cc_final: 0.8837 (p) REVERT: A 979 ASP cc_start: 0.8270 (t0) cc_final: 0.8016 (t0) REVERT: B 378 LYS cc_start: 0.8328 (ptpp) cc_final: 0.7983 (tppt) REVERT: B 493 GLN cc_start: 0.7260 (mp10) cc_final: 0.6947 (mp-120) REVERT: B 804 GLN cc_start: 0.8841 (mm110) cc_final: 0.8608 (mm110) REVERT: C 127 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.7297 (m) REVERT: C 333 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8364 (p) REVERT: C 462 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8408 (pttt) REVERT: C 505 TYR cc_start: 0.7661 (t80) cc_final: 0.7178 (t80) REVERT: C 574 ASP cc_start: 0.8159 (t70) cc_final: 0.7798 (t0) REVERT: C 902 MET cc_start: 0.9252 (mmm) cc_final: 0.8830 (mmt) REVERT: C 988 GLU cc_start: 0.8589 (mp0) cc_final: 0.7933 (mp0) REVERT: D 101 GLN cc_start: 0.8742 (mp10) cc_final: 0.8351 (mp10) REVERT: E 46 GLU cc_start: 0.7687 (tt0) cc_final: 0.7145 (tm-30) REVERT: E 100 ARG cc_start: 0.7947 (mmm-85) cc_final: 0.7511 (mtm-85) REVERT: F 4 MET cc_start: 0.5714 (OUTLIER) cc_final: 0.5502 (mmm) REVERT: F 11 LEU cc_start: 0.8405 (mp) cc_final: 0.7876 (tp) REVERT: F 24 ARG cc_start: 0.6855 (ttm110) cc_final: 0.6055 (mtm-85) REVERT: H 21 ILE cc_start: 0.7512 (mm) cc_final: 0.7302 (mp) REVERT: H 82 ASP cc_start: 0.7609 (m-30) cc_final: 0.7376 (m-30) REVERT: H 83 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7257 (p90) outliers start: 53 outliers final: 37 residues processed: 354 average time/residue: 0.4099 time to fit residues: 238.4374 Evaluate side-chains 334 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 314 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 269 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 139 optimal weight: 0.0470 overall best weight: 1.0882 ------------------------------------------------------------------------------- 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** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.128272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083472 restraints weight = 56435.974| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.60 r_work: 0.2997 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31226 Z= 0.133 Angle : 0.569 13.880 42642 Z= 0.285 Chirality : 0.045 0.459 4984 Planarity : 0.004 0.061 5398 Dihedral : 5.117 56.859 5478 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.19 % Allowed : 12.13 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.45 (0.14), residues: 3757 helix: 1.95 (0.22), residues: 659 sheet: 0.10 (0.16), residues: 1036 loop : -1.31 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 53 HIS 0.003 0.001 HIS B1088 PHE 0.021 0.001 PHE C 565 TYR 0.021 0.001 TYR B 453 ARG 0.007 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 48) link_NAG-ASN : angle 2.58024 ( 144) link_BETA1-4 : bond 0.00343 ( 18) link_BETA1-4 : angle 1.20734 ( 54) hydrogen bonds : bond 0.04497 ( 1094) hydrogen bonds : angle 5.11014 ( 3057) SS BOND : bond 0.00401 ( 43) SS BOND : angle 1.28380 ( 86) covalent geometry : bond 0.00317 (31117) covalent geometry : angle 0.54643 (42358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 310 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8399 (m-80) cc_final: 0.8176 (m-80) REVERT: A 646 ARG cc_start: 0.8262 (tpm170) cc_final: 0.7853 (tpp-160) REVERT: A 725 GLU cc_start: 0.8869 (tt0) cc_final: 0.8649 (tt0) REVERT: A 745 ASP cc_start: 0.7840 (t0) cc_final: 0.7347 (t0) REVERT: A 760 CYS cc_start: 0.9122 (m) cc_final: 0.8844 (p) REVERT: A 979 ASP cc_start: 0.8304 (t0) cc_final: 0.8037 (t0) REVERT: B 102 ARG cc_start: 0.6817 (mmp80) cc_final: 0.6540 (mmp80) REVERT: B 378 LYS cc_start: 0.8347 (ptpp) cc_final: 0.8022 (tppt) REVERT: B 408 ARG cc_start: 0.7755 (mmm160) cc_final: 0.7521 (mmm160) REVERT: C 333 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8416 (p) REVERT: C 574 ASP cc_start: 0.8116 (t70) cc_final: 0.7705 (t0) REVERT: C 675 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6486 (tm130) REVERT: C 902 MET cc_start: 0.9238 (mmm) cc_final: 0.8814 (mmt) REVERT: C 988 GLU cc_start: 0.8642 (mp0) cc_final: 0.7978 (mp0) REVERT: D 6 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6339 (tp40) REVERT: D 101 GLN cc_start: 0.8713 (mp10) cc_final: 0.8508 (mp10) REVERT: E 46 GLU cc_start: 0.7710 (tt0) cc_final: 0.7213 (tm-30) REVERT: E 59 ASP cc_start: 0.7869 (t0) cc_final: 0.7665 (t0) REVERT: E 100 ARG cc_start: 0.7918 (mmm-85) cc_final: 0.7525 (mtm-85) REVERT: E 112 TYR cc_start: 0.6664 (m-80) cc_final: 0.6442 (m-80) REVERT: F 11 LEU cc_start: 0.8398 (mp) cc_final: 0.7849 (tp) REVERT: F 24 ARG cc_start: 0.6908 (ttm110) cc_final: 0.6092 (mtm-85) REVERT: G 39 GLN cc_start: 0.7205 (tm-30) cc_final: 0.6944 (tm-30) REVERT: H 21 ILE cc_start: 0.7346 (mm) cc_final: 0.7109 (mt) REVERT: H 24 ARG cc_start: 0.7212 (ttp80) cc_final: 0.6828 (mtp-110) REVERT: H 78 LEU cc_start: 0.7756 (mp) cc_final: 0.7549 (mp) REVERT: H 82 ASP cc_start: 0.7558 (m-30) cc_final: 0.7305 (m-30) REVERT: I 46 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6995 (mm-30) REVERT: I 83 MET cc_start: 0.7973 (mtm) cc_final: 0.7391 (mtm) REVERT: I 89 GLU cc_start: 0.6985 (pm20) cc_final: 0.6783 (pm20) outliers start: 71 outliers final: 42 residues processed: 361 average time/residue: 0.3903 time to fit residues: 230.5465 Evaluate side-chains 335 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 290 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 229 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 371 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN D 89 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.125757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.080939 restraints weight = 56873.336| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.60 r_work: 0.2948 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31226 Z= 0.208 Angle : 0.628 15.079 42642 Z= 0.315 Chirality : 0.047 0.490 4984 Planarity : 0.004 0.061 5398 Dihedral : 5.183 50.129 5478 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.31 % Allowed : 12.77 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3757 helix: 1.82 (0.22), residues: 660 sheet: -0.01 (0.16), residues: 1091 loop : -1.36 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 53 HIS 0.004 0.001 HIS B1088 PHE 0.028 0.002 PHE G 27 TYR 0.023 0.001 TYR H 92 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 48) link_NAG-ASN : angle 2.75186 ( 144) link_BETA1-4 : bond 0.00392 ( 18) link_BETA1-4 : angle 1.21780 ( 54) hydrogen bonds : bond 0.05346 ( 1094) hydrogen bonds : angle 5.18897 ( 3057) SS BOND : bond 0.00405 ( 43) SS BOND : angle 1.66392 ( 86) covalent geometry : bond 0.00507 (31117) covalent geometry : angle 0.60323 (42358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 302 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 SER cc_start: 0.8181 (t) cc_final: 0.7743 (t) REVERT: A 449 TYR cc_start: 0.8381 (m-80) cc_final: 0.8162 (m-80) REVERT: A 646 ARG cc_start: 0.8285 (tpm170) cc_final: 0.7978 (tpp-160) REVERT: A 745 ASP cc_start: 0.7952 (t0) cc_final: 0.7469 (t0) REVERT: A 760 CYS cc_start: 0.9133 (m) cc_final: 0.8870 (p) REVERT: A 979 ASP cc_start: 0.8310 (t0) cc_final: 0.8020 (t0) REVERT: B 378 LYS cc_start: 0.8388 (ptpp) cc_final: 0.8070 (tppt) REVERT: B 408 ARG cc_start: 0.7764 (mmm160) cc_final: 0.7520 (mmm160) REVERT: B 661 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8457 (tp30) REVERT: C 333 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8524 (p) REVERT: C 574 ASP cc_start: 0.8239 (t70) cc_final: 0.7776 (t0) REVERT: C 988 GLU cc_start: 0.8698 (mp0) cc_final: 0.8333 (mp0) REVERT: D 6 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6531 (tp40) REVERT: D 101 GLN cc_start: 0.8763 (mp10) cc_final: 0.8526 (mp10) REVERT: E 59 ASP cc_start: 0.7807 (t0) cc_final: 0.7449 (t0) REVERT: E 100 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7487 (mtt180) REVERT: E 112 TYR cc_start: 0.6836 (m-80) cc_final: 0.6603 (m-80) REVERT: F 6 GLN cc_start: 0.5833 (OUTLIER) cc_final: 0.5622 (tp40) REVERT: F 11 LEU cc_start: 0.8485 (mp) cc_final: 0.7969 (tp) REVERT: F 24 ARG cc_start: 0.6947 (ttm110) cc_final: 0.6348 (mtm-85) REVERT: G 58 ILE cc_start: 0.9071 (mt) cc_final: 0.8858 (tp) REVERT: G 103 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6758 (mm-30) REVERT: H 79 GLN cc_start: 0.7990 (mm110) cc_final: 0.7748 (mp10) REVERT: I 68 PHE cc_start: 0.7561 (m-10) cc_final: 0.7340 (m-10) REVERT: I 83 MET cc_start: 0.7726 (mtm) cc_final: 0.7450 (mtt) REVERT: I 89 GLU cc_start: 0.7115 (pm20) cc_final: 0.6872 (pm20) outliers start: 75 outliers final: 58 residues processed: 357 average time/residue: 0.5527 time to fit residues: 325.3493 Evaluate side-chains 343 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 281 time to evaluate : 3.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 320 optimal weight: 0.0070 chunk 357 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN G 3 GLN G 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.127593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.083111 restraints weight = 56477.266| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.60 r_work: 0.2988 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31226 Z= 0.116 Angle : 0.574 14.130 42642 Z= 0.286 Chirality : 0.045 0.446 4984 Planarity : 0.004 0.060 5398 Dihedral : 4.960 47.179 5478 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.97 % Allowed : 13.79 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (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: -0.46 (0.14), residues: 3757 helix: 1.91 (0.22), residues: 667 sheet: 0.15 (0.16), residues: 1035 loop : -1.35 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 53 HIS 0.002 0.001 HIS I 35 PHE 0.031 0.001 PHE G 27 TYR 0.022 0.001 TYR B 453 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 48) link_NAG-ASN : angle 2.56205 ( 144) link_BETA1-4 : bond 0.00361 ( 18) link_BETA1-4 : angle 1.23509 ( 54) hydrogen bonds : bond 0.04417 ( 1094) hydrogen bonds : angle 5.00227 ( 3057) SS BOND : bond 0.00307 ( 43) SS BOND : angle 1.31447 ( 86) covalent geometry : bond 0.00272 (31117) covalent geometry : angle 0.55134 (42358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 305 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 SER cc_start: 0.8084 (t) cc_final: 0.7624 (t) REVERT: A 449 TYR cc_start: 0.8391 (m-80) cc_final: 0.8162 (m-80) REVERT: A 646 ARG cc_start: 0.8259 (tpm170) cc_final: 0.7955 (tpp-160) REVERT: A 745 ASP cc_start: 0.7935 (t0) cc_final: 0.7445 (t0) REVERT: A 760 CYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8848 (p) REVERT: A 979 ASP cc_start: 0.8298 (t0) cc_final: 0.8005 (t0) REVERT: B 102 ARG cc_start: 0.6898 (mmp80) cc_final: 0.6618 (mmp80) REVERT: B 378 LYS cc_start: 0.8374 (ptpp) cc_final: 0.8112 (tppt) REVERT: B 408 ARG cc_start: 0.7795 (mmm160) cc_final: 0.7548 (mmm160) REVERT: C 333 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8502 (p) REVERT: C 574 ASP cc_start: 0.8166 (t70) cc_final: 0.7614 (t0) REVERT: C 858 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8491 (pp) REVERT: C 988 GLU cc_start: 0.8668 (mp0) cc_final: 0.7992 (mp0) REVERT: D 6 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6546 (tp40) REVERT: D 101 GLN cc_start: 0.8683 (mp10) cc_final: 0.8410 (mp10) REVERT: E 13 GLN cc_start: 0.8607 (tp40) cc_final: 0.8293 (mm-40) REVERT: E 46 GLU cc_start: 0.7687 (tt0) cc_final: 0.7141 (tm-30) REVERT: E 59 ASP cc_start: 0.7844 (t0) cc_final: 0.7474 (t0) REVERT: E 100 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7454 (mtt180) REVERT: F 11 LEU cc_start: 0.8464 (mp) cc_final: 0.7940 (tp) REVERT: F 24 ARG cc_start: 0.6923 (ttm110) cc_final: 0.6250 (mtm-85) REVERT: G 58 ILE cc_start: 0.9070 (mt) cc_final: 0.8860 (tp) REVERT: G 103 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6739 (mm-30) REVERT: H 4 MET cc_start: 0.7456 (mmm) cc_final: 0.7032 (mmm) REVERT: I 19 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.7004 (ttm-80) REVERT: I 68 PHE cc_start: 0.7401 (m-10) cc_final: 0.6958 (m-80) REVERT: I 89 GLU cc_start: 0.7294 (pm20) cc_final: 0.7024 (pm20) outliers start: 64 outliers final: 46 residues processed: 351 average time/residue: 0.5703 time to fit residues: 336.5119 Evaluate side-chains 335 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 285 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 111 optimal weight: 9.9990 chunk 338 optimal weight: 30.0000 chunk 299 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 360 optimal weight: 9.9990 chunk 318 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.126537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.081977 restraints weight = 56577.570| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.59 r_work: 0.2980 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31226 Z= 0.159 Angle : 0.603 14.465 42642 Z= 0.299 Chirality : 0.046 0.458 4984 Planarity : 0.004 0.059 5398 Dihedral : 4.894 45.761 5478 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.03 % Allowed : 14.10 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3757 helix: 1.88 (0.22), residues: 667 sheet: 0.12 (0.16), residues: 1043 loop : -1.35 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 53 HIS 0.003 0.001 HIS G 35 PHE 0.030 0.001 PHE G 27 TYR 0.022 0.001 TYR B 453 ARG 0.005 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 48) link_NAG-ASN : angle 2.61788 ( 144) link_BETA1-4 : bond 0.00320 ( 18) link_BETA1-4 : angle 1.22897 ( 54) hydrogen bonds : bond 0.04720 ( 1094) hydrogen bonds : angle 5.00151 ( 3057) SS BOND : bond 0.00333 ( 43) SS BOND : angle 1.41553 ( 86) covalent geometry : bond 0.00388 (31117) covalent geometry : angle 0.57988 (42358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 298 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 SER cc_start: 0.8155 (t) cc_final: 0.7700 (t) REVERT: A 449 TYR cc_start: 0.8402 (m-80) cc_final: 0.8175 (m-80) REVERT: A 646 ARG cc_start: 0.8235 (tpm170) cc_final: 0.7942 (tpp-160) REVERT: A 745 ASP cc_start: 0.7956 (t0) cc_final: 0.7467 (t0) REVERT: A 760 CYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 979 ASP cc_start: 0.8310 (t0) cc_final: 0.8019 (t0) REVERT: B 378 LYS cc_start: 0.8383 (ptpp) cc_final: 0.8122 (tppt) REVERT: B 408 ARG cc_start: 0.7741 (mmm160) cc_final: 0.7499 (mmm160) REVERT: C 333 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8479 (p) REVERT: C 574 ASP cc_start: 0.8164 (t70) cc_final: 0.7744 (t0) REVERT: C 858 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8512 (pp) REVERT: C 988 GLU cc_start: 0.8680 (mp0) cc_final: 0.8317 (mp0) REVERT: D 6 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6578 (tp40) REVERT: D 101 GLN cc_start: 0.8631 (mp10) cc_final: 0.8354 (mp10) REVERT: E 13 GLN cc_start: 0.8638 (tp40) cc_final: 0.8337 (mm-40) REVERT: E 59 ASP cc_start: 0.7835 (t0) cc_final: 0.7382 (t0) REVERT: E 100 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7468 (mtt180) REVERT: F 11 LEU cc_start: 0.8478 (mp) cc_final: 0.7953 (tp) REVERT: F 24 ARG cc_start: 0.6824 (ttm110) cc_final: 0.6148 (mtm-85) REVERT: H 4 MET cc_start: 0.7242 (mmm) cc_final: 0.6551 (mmm) REVERT: I 19 ARG cc_start: 0.7467 (ttm-80) cc_final: 0.6993 (ttm-80) REVERT: I 83 MET cc_start: 0.7881 (mtt) cc_final: 0.7301 (mtt) REVERT: I 89 GLU cc_start: 0.7360 (pm20) cc_final: 0.7082 (pm20) outliers start: 66 outliers final: 55 residues processed: 345 average time/residue: 0.5604 time to fit residues: 318.9674 Evaluate side-chains 347 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 6.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR 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 740 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 235 optimal weight: 0.9990 chunk 270 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 348 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 203 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 355 optimal weight: 0.0670 chunk 195 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.128116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083874 restraints weight = 56253.275| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.59 r_work: 0.3002 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31226 Z= 0.109 Angle : 0.574 13.719 42642 Z= 0.284 Chirality : 0.044 0.431 4984 Planarity : 0.004 0.059 5398 Dihedral : 4.698 47.304 5478 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.88 % Allowed : 14.44 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3757 helix: 2.07 (0.22), residues: 656 sheet: 0.19 (0.16), residues: 1035 loop : -1.31 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 53 HIS 0.002 0.000 HIS G 35 PHE 0.029 0.001 PHE G 27 TYR 0.024 0.001 TYR B 453 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 48) link_NAG-ASN : angle 2.48559 ( 144) link_BETA1-4 : bond 0.00376 ( 18) link_BETA1-4 : angle 1.26496 ( 54) hydrogen bonds : bond 0.04090 ( 1094) hydrogen bonds : angle 4.85232 ( 3057) SS BOND : bond 0.00328 ( 43) SS BOND : angle 1.14493 ( 86) covalent geometry : bond 0.00254 (31117) covalent geometry : angle 0.55268 (42358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3376 (tmm) cc_final: 0.1674 (ptm) REVERT: A 438 SER cc_start: 0.8105 (t) cc_final: 0.7647 (t) REVERT: A 449 TYR cc_start: 0.8396 (m-80) cc_final: 0.8179 (m-80) REVERT: A 646 ARG cc_start: 0.8171 (tpm170) cc_final: 0.7880 (tpp-160) REVERT: A 745 ASP cc_start: 0.7921 (t0) cc_final: 0.7437 (t0) REVERT: A 760 CYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8835 (p) REVERT: A 979 ASP cc_start: 0.8287 (t0) cc_final: 0.8068 (t0) REVERT: B 81 ASN cc_start: 0.7735 (p0) cc_final: 0.7145 (p0) REVERT: B 102 ARG cc_start: 0.6889 (mmp80) cc_final: 0.6626 (mmp80) REVERT: B 346 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7938 (mtp85) REVERT: B 378 LYS cc_start: 0.8361 (ptpp) cc_final: 0.8122 (tppt) REVERT: B 408 ARG cc_start: 0.7763 (mmm160) cc_final: 0.7528 (mmm160) REVERT: C 333 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8468 (p) REVERT: C 574 ASP cc_start: 0.8084 (t70) cc_final: 0.7705 (t0) REVERT: C 814 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7573 (mmmt) REVERT: C 858 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8497 (pp) REVERT: C 988 GLU cc_start: 0.8648 (mp0) cc_final: 0.7991 (mp0) REVERT: D 6 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6524 (tp40) REVERT: E 13 GLN cc_start: 0.8678 (tp40) cc_final: 0.8426 (mm-40) REVERT: E 59 ASP cc_start: 0.7819 (t0) cc_final: 0.7357 (t0) REVERT: E 100 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7612 (mtt180) REVERT: E 112 TYR cc_start: 0.6892 (m-80) cc_final: 0.6578 (m-80) REVERT: F 11 LEU cc_start: 0.8484 (mp) cc_final: 0.7968 (tp) REVERT: F 24 ARG cc_start: 0.6681 (ttm110) cc_final: 0.5944 (mtm-85) REVERT: G 38 ARG cc_start: 0.6093 (ttp-170) cc_final: 0.5709 (ttp-170) REVERT: H 83 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6998 (p90) REVERT: I 19 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.7141 (ttm-80) REVERT: I 32 TYR cc_start: 0.8312 (m-80) cc_final: 0.8046 (m-80) REVERT: I 112 TYR cc_start: 0.8041 (m-80) cc_final: 0.7821 (m-80) outliers start: 61 outliers final: 48 residues processed: 346 average time/residue: 0.4239 time to fit residues: 242.8715 Evaluate side-chains 342 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 289 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 362 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 288 optimal weight: 0.7980 chunk 249 optimal weight: 3.9990 chunk 7 optimal weight: 0.0270 chunk 126 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 157 optimal weight: 0.4980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.128493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.084328 restraints weight = 56130.211| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.58 r_work: 0.3015 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 31226 Z= 0.105 Angle : 0.569 13.383 42642 Z= 0.281 Chirality : 0.044 0.428 4984 Planarity : 0.004 0.059 5398 Dihedral : 4.539 46.728 5478 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.54 % Allowed : 14.99 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3757 helix: 2.15 (0.22), residues: 657 sheet: 0.28 (0.16), residues: 1035 loop : -1.28 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 53 HIS 0.003 0.000 HIS I 35 PHE 0.030 0.001 PHE G 27 TYR 0.027 0.001 TYR A 505 ARG 0.005 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 48) link_NAG-ASN : angle 2.43614 ( 144) link_BETA1-4 : bond 0.00378 ( 18) link_BETA1-4 : angle 1.27263 ( 54) hydrogen bonds : bond 0.03896 ( 1094) hydrogen bonds : angle 4.76771 ( 3057) SS BOND : bond 0.00279 ( 43) SS BOND : angle 1.12280 ( 86) covalent geometry : bond 0.00246 (31117) covalent geometry : angle 0.54926 (42358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 293 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3412 (tmm) cc_final: 0.1738 (ptm) REVERT: A 438 SER cc_start: 0.8103 (t) cc_final: 0.7649 (t) REVERT: A 449 TYR cc_start: 0.8419 (m-80) cc_final: 0.8200 (m-80) REVERT: A 646 ARG cc_start: 0.8135 (tpm170) cc_final: 0.7841 (tpp-160) REVERT: A 745 ASP cc_start: 0.7900 (t0) cc_final: 0.7417 (t0) REVERT: A 760 CYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8823 (p) REVERT: A 979 ASP cc_start: 0.8307 (t0) cc_final: 0.8094 (t0) REVERT: B 81 ASN cc_start: 0.7739 (p0) cc_final: 0.7160 (p0) REVERT: B 102 ARG cc_start: 0.6894 (mmp80) cc_final: 0.6570 (mmp80) REVERT: B 378 LYS cc_start: 0.8370 (ptpp) cc_final: 0.8141 (tppt) REVERT: B 408 ARG cc_start: 0.7738 (mmm160) cc_final: 0.7514 (mmm160) REVERT: C 127 VAL cc_start: 0.7885 (OUTLIER) cc_final: 0.7616 (m) REVERT: C 574 ASP cc_start: 0.8128 (t70) cc_final: 0.7725 (t0) REVERT: C 814 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7608 (mmmt) REVERT: C 988 GLU cc_start: 0.8661 (mp0) cc_final: 0.8055 (mp0) REVERT: D 6 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6516 (tp40) REVERT: E 13 GLN cc_start: 0.8683 (tp40) cc_final: 0.8434 (mm-40) REVERT: E 59 ASP cc_start: 0.7830 (t0) cc_final: 0.7366 (t0) REVERT: E 100 ARG cc_start: 0.8118 (mmm-85) cc_final: 0.7659 (mtt180) REVERT: E 112 TYR cc_start: 0.6919 (m-80) cc_final: 0.6627 (m-80) REVERT: F 11 LEU cc_start: 0.8473 (mp) cc_final: 0.7954 (tp) REVERT: F 24 ARG cc_start: 0.6635 (ttm110) cc_final: 0.6035 (mtm180) REVERT: G 38 ARG cc_start: 0.6092 (ttp-170) cc_final: 0.5701 (ttp-170) REVERT: I 19 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7233 (ttm-80) outliers start: 50 outliers final: 45 residues processed: 328 average time/residue: 0.5405 time to fit residues: 297.1276 Evaluate side-chains 332 residues out of total 3318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 4.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 546 LEU 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 976 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 280 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 314 optimal weight: 0.0770 chunk 304 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 338 optimal weight: 20.0000 chunk 157 optimal weight: 0.4980 chunk 238 optimal weight: 6.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- 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** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.127537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.083210 restraints weight = 56233.163| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.59 r_work: 0.3005 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31226 Z= 0.130 Angle : 0.583 13.787 42642 Z= 0.288 Chirality : 0.045 0.437 4984 Planarity : 0.004 0.059 5398 Dihedral : 4.537 45.311 5478 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.82 % Allowed : 14.90 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3757 helix: 2.06 (0.22), residues: 666 sheet: 0.27 (0.16), residues: 1042 loop : -1.27 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 53 HIS 0.003 0.001 HIS A1064 PHE 0.030 0.001 PHE G 27 TYR 0.023 0.001 TYR B 453 ARG 0.005 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 48) link_NAG-ASN : angle 2.47182 ( 144) link_BETA1-4 : bond 0.00354 ( 18) link_BETA1-4 : angle 1.25874 ( 54) hydrogen bonds : bond 0.04180 ( 1094) hydrogen bonds : angle 4.79460 ( 3057) SS BOND : bond 0.00296 ( 43) SS BOND : angle 1.10752 ( 86) covalent geometry : bond 0.00314 (31117) covalent geometry : angle 0.56305 (42358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18756.11 seconds wall clock time: 336 minutes 24.79 seconds (20184.79 seconds total)