Starting phenix.real_space_refine on Fri Mar 6 05:17:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l2d_23125/03_2026/7l2d_23125.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2d_23125/03_2026/7l2d_23125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l2d_23125/03_2026/7l2d_23125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2d_23125/03_2026/7l2d_23125.map" model { file = "/net/cci-nas-00/data/ceres_data/7l2d_23125/03_2026/7l2d_23125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2d_23125/03_2026/7l2d_23125.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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 124 5.16 5 C 17985 2.51 5 N 4617 2.21 5 O 5602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28328 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1100, 8564 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 1100, 8564 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 8737 Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 971 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 799 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "B" Number of atoms: 8449 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1078, 8439 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 54, 'TRANS': 1023} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1078, 8439 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 54, 'TRANS': 1023} Chain breaks: 5 bond proxies already assigned to first conformer: 8625 Chain: "C" Number of atoms: 8451 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1078, 8439 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 54, 'TRANS': 1023} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1078, 8439 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 54, 'TRANS': 1023} Chain breaks: 5 bond proxies already assigned to first conformer: 8622 Chain: "D" 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: "E" 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: "F" 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: "G" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR A 365 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 365 " occ=0.50 residue: pdb=" N ATYR A 369 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 369 " occ=0.50 Time building chain proxies: 10.87, per 1000 atoms: 0.38 Number of scatterers: 28328 At special positions: 0 Unit cell: (143.38, 182.97, 185.11, 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 124 16.00 O 5602 8.00 N 4617 7.00 C 17985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, 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=2.15 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 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 S 2 " - " BMA S 3 " " 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 Y 2 " - " BMA Y 3 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 149 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 17 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 17 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 149 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 343 " " NAG B1311 " - " ASN B 603 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 149 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 17 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG I 1 " - " ASN A 122 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 165 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 165 " " NAG S 1 " - " ASN B 234 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " " NAG X 1 " - " ASN C 122 " " NAG Y 1 " - " ASN C 234 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 2.2 seconds 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6534 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 55 sheets defined 23.1% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.517A pdb=" N GLU A 180 " --> pdb=" O MET A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.716A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.564A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 783 removed outlier: 5.796A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.818A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 884 through 888 removed outlier: 4.204A pdb=" N THR A 887 " --> pdb=" O SER A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.423A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 967 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.694A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.394A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.785A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'L' and resid 27B through 30 removed outlier: 3.546A pdb=" N TYR L 30 " --> pdb=" O VAL L 27C" (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.553A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.868A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.733A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 630 through 638 removed outlier: 4.353A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 748 through 783 removed outlier: 5.806A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.924A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 4.011A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.524A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.553A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.596A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.088A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.015A 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 337 through 344 Processing helix chain 'C' and resid 365 through 372 removed outlier: 4.171A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 568 through 572 removed outlier: 4.108A pdb=" N THR C 572 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.941A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 748 through 783 removed outlier: 5.815A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.549A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.696A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.501A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.161A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.838A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.615A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.317A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.307A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.307A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.097A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 5.954A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.173A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 68 through 71 removed outlier: 6.236A pdb=" N HIS A 69 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS A 77 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.524A pdb=" N VAL A 143 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.499A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 10.773A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.667A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.882A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.448A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.928A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.492A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.888A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.869A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (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 1122 removed outlier: 3.527A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.681A pdb=" N VAL H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET H 80 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'H' and resid 32 through 39 Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.538A pdb=" N VAL L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AC7, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AC8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.523A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.019A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.418A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.168A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.815A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.498A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.168A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.979A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.108A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.106A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.908A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.782A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'B' and resid 1094 through 1098 Processing sheet with id=AE5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.004A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.545A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.750A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.557A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.016A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.453A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.191A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.654A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.101A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 796 through 797 Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.787A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1094 through 1097 1069 hydrogen bonds defined for protein. 2895 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.95 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4564 1.32 - 1.44: 8252 1.44 - 1.57: 15998 1.57 - 1.70: 1 1.70 - 1.82: 160 Bond restraints: 28975 Sorted by residual: bond pdb=" C TYR C 365 " pdb=" O TYR C 365 " ideal model delta sigma weight residual 1.236 1.362 -0.126 1.29e-02 6.01e+03 9.60e+01 bond pdb=" C TYR B 365 " pdb=" O TYR B 365 " ideal model delta sigma weight residual 1.236 1.358 -0.122 1.29e-02 6.01e+03 8.97e+01 bond pdb=" C PRO B 792 " pdb=" N PRO B 793 " ideal model delta sigma weight residual 1.328 1.382 -0.054 1.25e-02 6.40e+03 1.85e+01 bond pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.73e+01 bond pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.57e+01 ... (remaining 28970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 38252 2.75 - 5.50: 1108 5.50 - 8.25: 80 8.25 - 11.00: 12 11.00 - 13.75: 6 Bond angle restraints: 39458 Sorted by residual: angle pdb=" O TYR B 365 " pdb=" C TYR B 365 " pdb=" CA BTYR B 365 " ideal model delta sigma weight residual 119.38 133.13 -13.75 1.23e+00 6.61e-01 1.25e+02 angle pdb=" O TYR C 365 " pdb=" C TYR C 365 " pdb=" CA BTYR C 365 " ideal model delta sigma weight residual 119.38 132.63 -13.25 1.23e+00 6.61e-01 1.16e+02 angle pdb=" O TYR B 365 " pdb=" C TYR B 365 " pdb=" CA ATYR B 365 " ideal model delta sigma weight residual 119.05 132.75 -13.70 1.30e+00 5.92e-01 1.11e+02 angle pdb=" O TYR C 365 " pdb=" C TYR C 365 " pdb=" CA ATYR C 365 " ideal model delta sigma weight residual 119.05 132.45 -13.40 1.30e+00 5.92e-01 1.06e+02 angle pdb=" N GLN A 218 " pdb=" CA GLN A 218 " pdb=" C GLN A 218 " ideal model delta sigma weight residual 113.19 104.21 8.98 1.19e+00 7.06e-01 5.69e+01 ... (remaining 39453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 17163 21.50 - 43.00: 891 43.00 - 64.49: 120 64.49 - 85.99: 47 85.99 - 107.49: 14 Dihedral angle restraints: 18235 sinusoidal: 8053 harmonic: 10182 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -173.34 87.34 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 169.05 -76.05 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 159.59 -66.59 1 1.00e+01 1.00e-02 5.79e+01 ... (remaining 18232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.284: 4656 0.284 - 0.568: 22 0.568 - 0.852: 2 0.852 - 1.136: 2 1.136 - 1.420: 3 Chirality restraints: 4685 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.37e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.06e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.06e+02 ... (remaining 4682 not shown) Planarity restraints: 5057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.357 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG F 1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.153 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG A1304 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " -0.095 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1311 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG B1311 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG B1311 " 0.122 2.00e-02 2.50e+03 pdb=" N2 NAG B1311 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG B1311 " 0.149 2.00e-02 2.50e+03 ... (remaining 5054 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5694 2.78 - 3.31: 25590 3.31 - 3.84: 46610 3.84 - 4.37: 54075 4.37 - 4.90: 93056 Nonbonded interactions: 225025 Sorted by model distance: nonbonded pdb=" OG1 THR A 553 " pdb=" OD1 ASP A 586 " model vdw 2.252 3.040 nonbonded pdb=" OG SER A 884 " pdb=" OG1 THR A 887 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.276 3.040 nonbonded pdb=" OG SER C 673 " pdb=" OH TYR C 695 " model vdw 2.279 3.040 nonbonded pdb=" O ASP C 994 " pdb=" OG1 THR C 998 " model vdw 2.281 3.040 ... (remaining 225020 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 14 through 69 or resid 77 through 179 or resid 184 through \ 246 or resid 257 through 364 or resid 366 through 368 or resid 370 through 476 \ or resid 478 through 829 or resid 853 through 1311)) selection = (chain 'B' and (resid 14 through 178 or (resid 179 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 or (resid 185 through 186 and (name N o \ r name CA or name C or name O or name CB )) or resid 187 through 364 or resid 36 \ 6 through 368 or resid 370 through 476 or resid 478 through 1311)) selection = (chain 'C' and (resid 14 through 178 or (resid 179 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 or (resid 185 through 186 and (name N o \ r name CA or name C or name O or name CB )) or resid 187 through 364 or resid 36 \ 6 through 368 or resid 370 through 476 or resid 478 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'Y' } 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=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 36.460 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.006 0.126 29096 Z= 0.412 Angle : 1.074 15.731 39777 Z= 0.665 Chirality : 0.082 1.420 4685 Planarity : 0.017 0.305 5003 Dihedral : 13.258 107.491 11569 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.33 % Allowed : 2.01 % Favored : 97.66 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 3467 helix: -0.11 (0.18), residues: 701 sheet: 0.37 (0.18), residues: 766 loop : -0.88 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG C1000 TYR 0.027 0.002 TYR C 904 PHE 0.036 0.002 PHE B1121 TRP 0.019 0.002 TRP H 103 HIS 0.024 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00632 (28975) covalent geometry : angle 1.03342 (39458) SS BOND : bond 0.01808 ( 44) SS BOND : angle 1.29047 ( 88) hydrogen bonds : bond 0.16219 ( 1044) hydrogen bonds : angle 7.99001 ( 2895) link_BETA1-4 : bond 0.00408 ( 23) link_BETA1-4 : angle 2.61639 ( 69) link_NAG-ASN : bond 0.01394 ( 54) link_NAG-ASN : angle 4.39984 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 355 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8993 (m) cc_final: 0.8504 (p) REVERT: A 919 ASN cc_start: 0.8267 (m-40) cc_final: 0.7900 (t0) REVERT: H 72 ASP cc_start: 0.8032 (t70) cc_final: 0.7745 (t0) REVERT: H 85 GLU cc_start: 0.6012 (tp30) cc_final: 0.5601 (pm20) REVERT: H 100 MET cc_start: 0.5079 (pmm) cc_final: 0.4351 (ptp) REVERT: L 5 THR cc_start: 0.7765 (p) cc_final: 0.7562 (t) REVERT: L 95 THR cc_start: 0.4333 (m) cc_final: 0.3910 (p) REVERT: B 389 ASP cc_start: 0.7949 (t0) cc_final: 0.7411 (t0) REVERT: B 571 ASP cc_start: 0.7300 (p0) cc_final: 0.6909 (p0) REVERT: B 886 TRP cc_start: 0.7313 (p90) cc_final: 0.7044 (p90) REVERT: B 934 ILE cc_start: 0.8997 (mm) cc_final: 0.8720 (mm) REVERT: C 139 PRO cc_start: 0.8731 (Cg_exo) cc_final: 0.8483 (Cg_endo) REVERT: C 313 TYR cc_start: 0.8645 (m-80) cc_final: 0.8190 (m-80) REVERT: C 558 LYS cc_start: 0.7411 (mttt) cc_final: 0.7199 (tppt) REVERT: C 776 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8775 (ttpp) outliers start: 9 outliers final: 1 residues processed: 362 average time/residue: 0.1677 time to fit residues: 101.7294 Evaluate side-chains 210 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 134 GLN A 207 HIS ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 GLN B 388 ASN B 580 GLN B 804 GLN B 856 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 14 GLN C 787 GLN C 965 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.089358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068497 restraints weight = 145866.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.071155 restraints weight = 56120.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.072944 restraints weight = 31931.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073960 restraints weight = 22411.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074726 restraints weight = 18132.564| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 29096 Z= 0.249 Angle : 0.735 15.959 39777 Z= 0.363 Chirality : 0.048 0.340 4685 Planarity : 0.005 0.070 5003 Dihedral : 7.863 69.642 5377 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.15 % Allowed : 7.89 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 3467 helix: 0.51 (0.19), residues: 740 sheet: 0.26 (0.18), residues: 778 loop : -0.76 (0.13), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 34 TYR 0.029 0.002 TYR B1067 PHE 0.034 0.002 PHE B 55 TRP 0.034 0.002 TRP C 152 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00564 (28975) covalent geometry : angle 0.71197 (39458) SS BOND : bond 0.00335 ( 44) SS BOND : angle 1.00120 ( 88) hydrogen bonds : bond 0.04512 ( 1044) hydrogen bonds : angle 6.27667 ( 2895) link_BETA1-4 : bond 0.00399 ( 23) link_BETA1-4 : angle 2.57266 ( 69) link_NAG-ASN : bond 0.00394 ( 54) link_NAG-ASN : angle 2.40595 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9019 (m) cc_final: 0.8476 (p) REVERT: H 85 GLU cc_start: 0.5831 (tp30) cc_final: 0.5359 (pm20) REVERT: H 100 MET cc_start: 0.5654 (pmm) cc_final: 0.4878 (ptp) REVERT: L 61 ARG cc_start: 0.6718 (ptp-110) cc_final: 0.6460 (mtt180) REVERT: B 175 PHE cc_start: 0.5857 (p90) cc_final: 0.5645 (p90) REVERT: B 707 TYR cc_start: 0.7117 (t80) cc_final: 0.6508 (t80) REVERT: B 886 TRP cc_start: 0.7517 (p90) cc_final: 0.6952 (p90) REVERT: B 902 MET cc_start: 0.8900 (mmp) cc_final: 0.8623 (mmt) REVERT: C 558 LYS cc_start: 0.7456 (mttt) cc_final: 0.7156 (tppt) outliers start: 34 outliers final: 26 residues processed: 232 average time/residue: 0.1696 time to fit residues: 66.3243 Evaluate side-chains 203 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 317 optimal weight: 0.9990 chunk 316 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS A 856 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.087800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.066847 restraints weight = 157616.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.069524 restraints weight = 59921.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.071308 restraints weight = 33794.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.072369 restraints weight = 23565.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.073088 restraints weight = 18910.810| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29096 Z= 0.203 Angle : 0.648 10.240 39777 Z= 0.326 Chirality : 0.046 0.268 4685 Planarity : 0.004 0.060 5003 Dihedral : 6.741 59.829 5375 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.55 % Allowed : 9.14 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3467 helix: 0.80 (0.19), residues: 734 sheet: 0.12 (0.18), residues: 793 loop : -0.70 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.025 0.002 TYR C 369 PHE 0.025 0.002 PHE B 55 TRP 0.032 0.002 TRP C 152 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00465 (28975) covalent geometry : angle 0.63056 (39458) SS BOND : bond 0.00273 ( 44) SS BOND : angle 0.76185 ( 88) hydrogen bonds : bond 0.04175 ( 1044) hydrogen bonds : angle 5.90743 ( 2895) link_BETA1-4 : bond 0.00607 ( 23) link_BETA1-4 : angle 2.38553 ( 69) link_NAG-ASN : bond 0.00306 ( 54) link_NAG-ASN : angle 1.90122 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8165 (ptt) cc_final: 0.7923 (pmm) REVERT: A 900 MET cc_start: 0.8486 (mtt) cc_final: 0.8127 (mtp) REVERT: A 965 GLN cc_start: 0.8780 (tp40) cc_final: 0.8447 (tp-100) REVERT: A 1050 MET cc_start: 0.8185 (mtm) cc_final: 0.7940 (mtm) REVERT: H 59 TYR cc_start: 0.4766 (OUTLIER) cc_final: 0.4358 (m-80) REVERT: H 100 TYR cc_start: 0.8688 (t80) cc_final: 0.8462 (t80) REVERT: H 100 MET cc_start: 0.6155 (pmm) cc_final: 0.5007 (ptp) REVERT: H 103 TRP cc_start: 0.8034 (m-10) cc_final: 0.7740 (m-10) REVERT: L 91 TYR cc_start: 0.6259 (t80) cc_final: 0.6044 (t80) REVERT: B 707 TYR cc_start: 0.7417 (t80) cc_final: 0.6886 (t80) REVERT: B 886 TRP cc_start: 0.7570 (p90) cc_final: 0.7026 (p90) REVERT: C 558 LYS cc_start: 0.7468 (mttt) cc_final: 0.7119 (tppt) REVERT: C 902 MET cc_start: 0.9122 (tpp) cc_final: 0.8911 (tpt) outliers start: 46 outliers final: 30 residues processed: 232 average time/residue: 0.1635 time to fit residues: 66.5402 Evaluate side-chains 208 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 306 optimal weight: 6.9990 chunk 277 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 236 optimal weight: 8.9990 chunk 188 optimal weight: 0.9980 chunk 55 optimal weight: 0.0050 chunk 19 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 901 GLN A1108 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** 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 = 0.3461 r_free = 0.3461 target = 0.088557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.067710 restraints weight = 157099.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.070393 restraints weight = 59051.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072194 restraints weight = 33191.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073328 restraints weight = 23157.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.073976 restraints weight = 18441.873| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29096 Z= 0.136 Angle : 0.584 10.070 39777 Z= 0.293 Chirality : 0.044 0.265 4685 Planarity : 0.004 0.055 5003 Dihedral : 6.047 59.776 5375 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.25 % Allowed : 10.62 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3467 helix: 1.01 (0.19), residues: 735 sheet: 0.25 (0.18), residues: 768 loop : -0.66 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.024 0.001 TYR H 100G PHE 0.030 0.001 PHE B 175 TRP 0.044 0.002 TRP C 152 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00307 (28975) covalent geometry : angle 0.56717 (39458) SS BOND : bond 0.00178 ( 44) SS BOND : angle 0.61806 ( 88) hydrogen bonds : bond 0.03803 ( 1044) hydrogen bonds : angle 5.63148 ( 2895) link_BETA1-4 : bond 0.00556 ( 23) link_BETA1-4 : angle 2.29955 ( 69) link_NAG-ASN : bond 0.00199 ( 54) link_NAG-ASN : angle 1.68654 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8228 (mm) REVERT: A 900 MET cc_start: 0.8320 (mtt) cc_final: 0.8059 (mtp) REVERT: A 965 GLN cc_start: 0.8726 (tp40) cc_final: 0.8437 (tp-100) REVERT: H 59 TYR cc_start: 0.4809 (OUTLIER) cc_final: 0.4480 (m-80) REVERT: H 100 TYR cc_start: 0.8643 (t80) cc_final: 0.8380 (t80) REVERT: H 100 MET cc_start: 0.6388 (pmm) cc_final: 0.4988 (ptp) REVERT: H 103 TRP cc_start: 0.8079 (m100) cc_final: 0.7682 (m-10) REVERT: B 707 TYR cc_start: 0.7346 (t80) cc_final: 0.6978 (t80) REVERT: B 886 TRP cc_start: 0.7555 (p90) cc_final: 0.7053 (p90) REVERT: C 558 LYS cc_start: 0.7421 (mttt) cc_final: 0.7091 (tppt) outliers start: 37 outliers final: 21 residues processed: 226 average time/residue: 0.1579 time to fit residues: 62.1956 Evaluate side-chains 206 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 83 optimal weight: 1.9990 chunk 174 optimal weight: 0.2980 chunk 344 optimal weight: 0.4980 chunk 265 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 286 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 245 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS B 784 GLN B 919 ASN ** B1048 HIS ** 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 = 0.3482 r_free = 0.3482 target = 0.089676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069239 restraints weight = 136188.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.071838 restraints weight = 54601.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073589 restraints weight = 31442.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.074594 restraints weight = 22162.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075348 restraints weight = 17958.832| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29096 Z= 0.104 Angle : 0.554 11.101 39777 Z= 0.279 Chirality : 0.043 0.256 4685 Planarity : 0.004 0.054 5003 Dihedral : 5.479 59.104 5375 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.28 % Allowed : 10.95 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3467 helix: 1.30 (0.19), residues: 712 sheet: 0.27 (0.18), residues: 770 loop : -0.58 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.020 0.001 TYR B1067 PHE 0.020 0.001 PHE C 562 TRP 0.025 0.001 TRP C 152 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00229 (28975) covalent geometry : angle 0.53974 (39458) SS BOND : bond 0.00132 ( 44) SS BOND : angle 0.56271 ( 88) hydrogen bonds : bond 0.03600 ( 1044) hydrogen bonds : angle 5.44619 ( 2895) link_BETA1-4 : bond 0.00596 ( 23) link_BETA1-4 : angle 2.19970 ( 69) link_NAG-ASN : bond 0.00233 ( 54) link_NAG-ASN : angle 1.50090 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8183 (mm) REVERT: A 900 MET cc_start: 0.8224 (mtt) cc_final: 0.7938 (mtp) REVERT: A 965 GLN cc_start: 0.8696 (tp40) cc_final: 0.8424 (tp-100) REVERT: H 59 TYR cc_start: 0.4826 (OUTLIER) cc_final: 0.4419 (m-80) REVERT: H 100 TYR cc_start: 0.8642 (t80) cc_final: 0.8280 (t80) REVERT: H 100 MET cc_start: 0.6538 (pmm) cc_final: 0.5283 (ptp) REVERT: H 103 TRP cc_start: 0.8084 (m100) cc_final: 0.7623 (m-10) REVERT: B 245 HIS cc_start: 0.4003 (OUTLIER) cc_final: 0.3695 (m-70) REVERT: B 707 TYR cc_start: 0.7289 (t80) cc_final: 0.6951 (t80) REVERT: B 731 MET cc_start: 0.8880 (ttp) cc_final: 0.8670 (ttp) REVERT: B 886 TRP cc_start: 0.7527 (p90) cc_final: 0.7018 (p90) REVERT: C 558 LYS cc_start: 0.7391 (mttt) cc_final: 0.7055 (tppt) outliers start: 38 outliers final: 23 residues processed: 229 average time/residue: 0.1596 time to fit residues: 62.9905 Evaluate side-chains 206 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 318 optimal weight: 5.9990 chunk 249 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 320 optimal weight: 4.9990 chunk 282 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 chunk 345 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN L 69 ASN B 207 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** 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 = 0.3433 r_free = 0.3433 target = 0.087006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.066400 restraints weight = 141131.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.068977 restraints weight = 56615.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.070689 restraints weight = 32826.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.071780 restraints weight = 23253.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.072391 restraints weight = 18702.086| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29096 Z= 0.200 Angle : 0.608 9.942 39777 Z= 0.308 Chirality : 0.044 0.242 4685 Planarity : 0.004 0.053 5003 Dihedral : 5.654 59.475 5375 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.25 % Allowed : 11.71 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3467 helix: 1.13 (0.19), residues: 726 sheet: 0.18 (0.18), residues: 790 loop : -0.58 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 246 TYR 0.020 0.002 TYR B1067 PHE 0.022 0.002 PHE C 562 TRP 0.019 0.002 TRP C 152 HIS 0.018 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00459 (28975) covalent geometry : angle 0.59296 (39458) SS BOND : bond 0.00270 ( 44) SS BOND : angle 0.64655 ( 88) hydrogen bonds : bond 0.03904 ( 1044) hydrogen bonds : angle 5.52971 ( 2895) link_BETA1-4 : bond 0.00519 ( 23) link_BETA1-4 : angle 2.21097 ( 69) link_NAG-ASN : bond 0.00294 ( 54) link_NAG-ASN : angle 1.72213 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8258 (mm) REVERT: A 900 MET cc_start: 0.8436 (mtt) cc_final: 0.8198 (mtp) REVERT: A 965 GLN cc_start: 0.8789 (tp40) cc_final: 0.8544 (tp-100) REVERT: H 48 MET cc_start: 0.5905 (ttm) cc_final: 0.5450 (ptt) REVERT: H 59 TYR cc_start: 0.4864 (OUTLIER) cc_final: 0.4485 (m-80) REVERT: H 100 TYR cc_start: 0.8659 (t80) cc_final: 0.8248 (t80) REVERT: H 100 MET cc_start: 0.6700 (pmm) cc_final: 0.5465 (ptp) REVERT: H 103 TRP cc_start: 0.8011 (m100) cc_final: 0.7644 (m-10) REVERT: B 707 TYR cc_start: 0.7429 (t80) cc_final: 0.7095 (t80) REVERT: B 886 TRP cc_start: 0.7470 (p90) cc_final: 0.6991 (p90) REVERT: C 902 MET cc_start: 0.9108 (tpp) cc_final: 0.8903 (tpp) outliers start: 37 outliers final: 27 residues processed: 204 average time/residue: 0.1495 time to fit residues: 52.5050 Evaluate side-chains 201 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 99 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 307 optimal weight: 0.7980 chunk 266 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 331 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.088545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.068086 restraints weight = 132002.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070705 restraints weight = 52806.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.072438 restraints weight = 30537.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073522 restraints weight = 21574.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.074137 restraints weight = 17385.622| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29096 Z= 0.116 Angle : 0.558 10.422 39777 Z= 0.281 Chirality : 0.044 0.266 4685 Planarity : 0.004 0.051 5003 Dihedral : 5.321 58.451 5375 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.15 % Allowed : 12.24 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3467 helix: 1.25 (0.19), residues: 734 sheet: 0.27 (0.18), residues: 773 loop : -0.54 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.019 0.001 TYR B1067 PHE 0.022 0.001 PHE C 562 TRP 0.017 0.001 TRP C 152 HIS 0.010 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00263 (28975) covalent geometry : angle 0.54458 (39458) SS BOND : bond 0.00153 ( 44) SS BOND : angle 0.53794 ( 88) hydrogen bonds : bond 0.03605 ( 1044) hydrogen bonds : angle 5.38439 ( 2895) link_BETA1-4 : bond 0.00568 ( 23) link_BETA1-4 : angle 2.09211 ( 69) link_NAG-ASN : bond 0.00193 ( 54) link_NAG-ASN : angle 1.48957 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8305 (mm) REVERT: A 900 MET cc_start: 0.8259 (mtt) cc_final: 0.8018 (mtp) REVERT: A 965 GLN cc_start: 0.8758 (tp40) cc_final: 0.8512 (tp-100) REVERT: H 79 TYR cc_start: 0.7426 (m-80) cc_final: 0.7144 (m-80) REVERT: H 100 TYR cc_start: 0.8627 (t80) cc_final: 0.8126 (t80) REVERT: H 100 MET cc_start: 0.6630 (pmm) cc_final: 0.5300 (ptp) REVERT: H 103 TRP cc_start: 0.7998 (m100) cc_final: 0.7644 (m-10) REVERT: B 707 TYR cc_start: 0.7447 (t80) cc_final: 0.7126 (t80) REVERT: B 731 MET cc_start: 0.8889 (ttp) cc_final: 0.8674 (ttp) REVERT: B 740 MET cc_start: 0.8941 (ttt) cc_final: 0.8696 (ttt) REVERT: B 886 TRP cc_start: 0.7512 (p90) cc_final: 0.6955 (p90) outliers start: 34 outliers final: 30 residues processed: 218 average time/residue: 0.1502 time to fit residues: 57.1076 Evaluate side-chains 212 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 284 optimal weight: 0.0980 chunk 58 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 229 optimal weight: 0.5980 chunk 324 optimal weight: 5.9990 chunk 179 optimal weight: 0.5980 chunk 127 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.089443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.068625 restraints weight = 157069.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.071404 restraints weight = 57708.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.073260 restraints weight = 32064.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.074415 restraints weight = 22193.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.075190 restraints weight = 17528.745| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29096 Z= 0.101 Angle : 0.543 10.476 39777 Z= 0.275 Chirality : 0.043 0.256 4685 Planarity : 0.004 0.051 5003 Dihedral : 5.023 57.238 5375 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.09 % Allowed : 12.43 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3467 helix: 1.32 (0.19), residues: 736 sheet: 0.31 (0.18), residues: 760 loop : -0.50 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.019 0.001 TYR B1067 PHE 0.022 0.001 PHE C 562 TRP 0.023 0.001 TRP H 36 HIS 0.009 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00223 (28975) covalent geometry : angle 0.53073 (39458) SS BOND : bond 0.00119 ( 44) SS BOND : angle 0.53469 ( 88) hydrogen bonds : bond 0.03477 ( 1044) hydrogen bonds : angle 5.26962 ( 2895) link_BETA1-4 : bond 0.00584 ( 23) link_BETA1-4 : angle 2.04656 ( 69) link_NAG-ASN : bond 0.00193 ( 54) link_NAG-ASN : angle 1.39529 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.785 Fit side-chains REVERT: A 569 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8217 (mm) REVERT: A 900 MET cc_start: 0.8227 (mtt) cc_final: 0.7981 (mtp) REVERT: A 962 LEU cc_start: 0.9197 (tt) cc_final: 0.8886 (tp) REVERT: A 965 GLN cc_start: 0.8745 (tp40) cc_final: 0.8492 (tp-100) REVERT: H 48 MET cc_start: 0.5247 (ptt) cc_final: 0.4974 (mtm) REVERT: H 59 TYR cc_start: 0.4554 (OUTLIER) cc_final: 0.4253 (m-80) REVERT: H 100 MET cc_start: 0.6647 (pmm) cc_final: 0.5344 (ptp) REVERT: H 103 TRP cc_start: 0.7994 (m100) cc_final: 0.7660 (m-10) REVERT: B 707 TYR cc_start: 0.7433 (t80) cc_final: 0.7175 (t80) REVERT: B 731 MET cc_start: 0.8848 (ttp) cc_final: 0.8619 (ttp) REVERT: B 740 MET cc_start: 0.8903 (ttt) cc_final: 0.8673 (ttt) REVERT: B 886 TRP cc_start: 0.7546 (p90) cc_final: 0.7005 (p90) REVERT: C 896 ILE cc_start: 0.9219 (mm) cc_final: 0.9015 (tp) outliers start: 32 outliers final: 27 residues processed: 221 average time/residue: 0.1503 time to fit residues: 57.4345 Evaluate side-chains 211 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 10 optimal weight: 3.9990 chunk 322 optimal weight: 0.9990 chunk 304 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 116 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** 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 = 0.3454 r_free = 0.3454 target = 0.088180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.067847 restraints weight = 139810.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.070463 restraints weight = 55737.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072182 restraints weight = 32079.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073284 restraints weight = 22593.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073889 restraints weight = 18114.354| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29096 Z= 0.140 Angle : 0.563 10.414 39777 Z= 0.286 Chirality : 0.043 0.242 4685 Planarity : 0.004 0.052 5003 Dihedral : 5.036 56.357 5375 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.15 % Allowed : 12.89 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3467 helix: 1.31 (0.19), residues: 734 sheet: 0.24 (0.18), residues: 777 loop : -0.47 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.019 0.001 TYR B1067 PHE 0.023 0.001 PHE C 562 TRP 0.043 0.001 TRP H 47 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00320 (28975) covalent geometry : angle 0.55028 (39458) SS BOND : bond 0.00180 ( 44) SS BOND : angle 0.62244 ( 88) hydrogen bonds : bond 0.03615 ( 1044) hydrogen bonds : angle 5.29972 ( 2895) link_BETA1-4 : bond 0.00529 ( 23) link_BETA1-4 : angle 2.05146 ( 69) link_NAG-ASN : bond 0.00183 ( 54) link_NAG-ASN : angle 1.48287 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 1.074 Fit side-chains REVERT: A 569 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8342 (mm) REVERT: A 900 MET cc_start: 0.8305 (mtt) cc_final: 0.8099 (mtp) REVERT: A 962 LEU cc_start: 0.9177 (tt) cc_final: 0.8860 (tp) REVERT: A 965 GLN cc_start: 0.8810 (tp40) cc_final: 0.8545 (tp-100) REVERT: H 38 ARG cc_start: 0.3988 (tpt-90) cc_final: 0.3762 (tpt-90) REVERT: H 100 MET cc_start: 0.6830 (pmm) cc_final: 0.5541 (ptp) REVERT: H 103 TRP cc_start: 0.8038 (m100) cc_final: 0.7646 (m-10) REVERT: B 707 TYR cc_start: 0.7484 (t80) cc_final: 0.7270 (t80) REVERT: B 740 MET cc_start: 0.8796 (ttt) cc_final: 0.8556 (ttt) outliers start: 34 outliers final: 30 residues processed: 203 average time/residue: 0.1572 time to fit residues: 55.5257 Evaluate side-chains 207 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 217 optimal weight: 7.9990 chunk 56 optimal weight: 0.0770 chunk 87 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 176 optimal weight: 0.0980 chunk 73 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 234 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.089723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069393 restraints weight = 133147.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.072034 restraints weight = 52697.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.073796 restraints weight = 30362.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074912 restraints weight = 21353.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075524 restraints weight = 17128.175| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29096 Z= 0.100 Angle : 0.546 10.724 39777 Z= 0.276 Chirality : 0.043 0.251 4685 Planarity : 0.004 0.050 5003 Dihedral : 4.779 53.145 5375 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.05 % Allowed : 12.89 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3467 helix: 1.36 (0.19), residues: 736 sheet: 0.35 (0.18), residues: 773 loop : -0.49 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.019 0.001 TYR L 87 PHE 0.040 0.001 PHE A 238 TRP 0.034 0.001 TRP H 47 HIS 0.009 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00220 (28975) covalent geometry : angle 0.53477 (39458) SS BOND : bond 0.00105 ( 44) SS BOND : angle 0.64377 ( 88) hydrogen bonds : bond 0.03430 ( 1044) hydrogen bonds : angle 5.19337 ( 2895) link_BETA1-4 : bond 0.00600 ( 23) link_BETA1-4 : angle 1.97425 ( 69) link_NAG-ASN : bond 0.00202 ( 54) link_NAG-ASN : angle 1.32855 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 1.054 Fit side-chains REVERT: A 569 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8304 (mm) REVERT: A 900 MET cc_start: 0.8184 (mtt) cc_final: 0.7973 (mtp) REVERT: A 962 LEU cc_start: 0.9168 (tt) cc_final: 0.8884 (tt) REVERT: H 100 MET cc_start: 0.6790 (pmm) cc_final: 0.5446 (ptp) REVERT: H 103 TRP cc_start: 0.7985 (m100) cc_final: 0.7612 (m-10) REVERT: B 707 TYR cc_start: 0.7495 (t80) cc_final: 0.7268 (t80) REVERT: B 731 MET cc_start: 0.8899 (ttp) cc_final: 0.8638 (ttp) REVERT: B 886 TRP cc_start: 0.7508 (p90) cc_final: 0.6921 (p90) REVERT: C 896 ILE cc_start: 0.9177 (mm) cc_final: 0.8962 (tp) outliers start: 31 outliers final: 28 residues processed: 218 average time/residue: 0.1650 time to fit residues: 62.0478 Evaluate side-chains 215 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 169 optimal weight: 0.0470 chunk 94 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 207 optimal weight: 0.0980 chunk 205 optimal weight: 4.9990 chunk 319 optimal weight: 3.9990 chunk 283 optimal weight: 0.0470 chunk 167 optimal weight: 0.9980 chunk 160 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 303 optimal weight: 8.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.090337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.070524 restraints weight = 119920.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073019 restraints weight = 50369.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074686 restraints weight = 29794.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075751 restraints weight = 21410.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.076345 restraints weight = 17299.023| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29096 Z= 0.098 Angle : 0.543 10.689 39777 Z= 0.273 Chirality : 0.043 0.246 4685 Planarity : 0.004 0.049 5003 Dihedral : 4.563 53.173 5375 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.95 % Allowed : 13.16 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3467 helix: 1.53 (0.20), residues: 716 sheet: 0.37 (0.18), residues: 775 loop : -0.41 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.030 0.001 TYR H 100F PHE 0.035 0.001 PHE A 238 TRP 0.025 0.001 TRP H 47 HIS 0.009 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00215 (28975) covalent geometry : angle 0.53184 (39458) SS BOND : bond 0.00093 ( 44) SS BOND : angle 0.58117 ( 88) hydrogen bonds : bond 0.03362 ( 1044) hydrogen bonds : angle 5.12842 ( 2895) link_BETA1-4 : bond 0.00574 ( 23) link_BETA1-4 : angle 1.93209 ( 69) link_NAG-ASN : bond 0.00188 ( 54) link_NAG-ASN : angle 1.29178 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5212.84 seconds wall clock time: 90 minutes 56.33 seconds (5456.33 seconds total)