Starting phenix.real_space_refine on Thu Mar 5 05:22:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vo0_21256/03_2026/6vo0_21256.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vo0_21256/03_2026/6vo0_21256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vo0_21256/03_2026/6vo0_21256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vo0_21256/03_2026/6vo0_21256.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vo0_21256/03_2026/6vo0_21256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vo0_21256/03_2026/6vo0_21256.map" } resolution = 3.52 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= 0.002 sd= 0.082 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 132 5.16 5 C 12225 2.51 5 N 3267 2.21 5 O 3870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.01s 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: 19494 Number of models: 1 Model: "" Number of chains: 36 Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 848 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 917 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "A" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3429 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "J" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 848 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "G" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 917 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "C" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3429 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 848 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 917 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3429 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" 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: "c" 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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.27, per 1000 atoms: 0.22 Number of scatterers: 19494 At special positions: 0 Unit cell: (165.83, 162.74, 146.26, 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 132 16.00 O 3870 8.00 N 3267 7.00 C 12225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35A" - pdb=" SG CYS G 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.10 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35A" - pdb=" SG CYS I 50 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.10 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.04 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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-ASN " NAG A 608 " - " ASN A 276 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 332 " " NAG A 613 " - " ASN A 386 " " NAG A 614 " - " ASN A 392 " " NAG A 617 " - " ASN A 363 " " NAG A 618 " - " ASN A 234 " " NAG A 619 " - " ASN A 197 " " NAG A 624 " - " ASN A 88 " " NAG C 608 " - " ASN C 276 " " NAG C 611 " - " ASN C 301 " " NAG C 612 " - " ASN C 332 " " NAG C 613 " - " ASN C 386 " " NAG C 614 " - " ASN C 392 " " NAG C 617 " - " ASN C 363 " " NAG C 618 " - " ASN C 234 " " NAG C 619 " - " ASN C 197 " " NAG C 624 " - " ASN C 88 " " NAG D 608 " - " ASN D 276 " " NAG D 611 " - " ASN D 301 " " NAG D 612 " - " ASN D 332 " " NAG D 613 " - " ASN D 386 " " NAG D 614 " - " ASN D 392 " " NAG D 617 " - " ASN D 363 " " NAG D 618 " - " ASN D 234 " " NAG D 619 " - " ASN D 197 " " NAG D 624 " - " ASN D 88 " " NAG M 1 " - " ASN A 133 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 448 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 137 " " NAG T 1 " - " ASN C 133 " " NAG U 1 " - " ASN C 160 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 295 " " NAG X 1 " - " ASN C 448 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 137 " " NAG a 1 " - " ASN D 133 " " NAG b 1 " - " ASN D 160 " " NAG c 1 " - " ASN D 262 " " NAG d 1 " - " ASN D 295 " " NAG e 1 " - " ASN D 448 " " NAG f 1 " - " ASN D 156 " " NAG g 1 " - " ASN D 137 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 706.0 milliseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 23.1% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'L' and resid 59 through 62 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.661A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.229A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.744A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 662 removed outlier: 4.780A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 62 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'C' and resid 98 through 115 removed outlier: 3.661A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.229A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.745A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 639 through 662 removed outlier: 4.781A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 62 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'D' and resid 98 through 115 removed outlier: 3.661A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 354 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 381 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 476 through 481 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.228A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.744A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 662 removed outlier: 4.780A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 14 removed outlier: 4.675A pdb=" N GLY L 100 " --> pdb=" O CYS L 88 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER H 96 " --> pdb=" O VAL H 100H" (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL H 100H" --> pdb=" O SER H 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 removed outlier: 7.466A pdb=" N VAL A 242 " --> pdb=" O HIS A 85 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N HIS A 85 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AB2, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AB3, first strand: chain 'A' and resid 158 through 162 Processing sheet with id=AB4, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.116A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.425A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.459A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.906A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'J' and resid 10 through 14 removed outlier: 4.674A pdb=" N GLY J 100 " --> pdb=" O CYS J 88 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.392A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER G 96 " --> pdb=" O VAL G 100H" (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL G 100H" --> pdb=" O SER G 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.392A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 7.466A pdb=" N VAL C 242 " --> pdb=" O HIS C 85 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N HIS C 85 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC9, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AD1, first strand: chain 'C' and resid 158 through 162 Processing sheet with id=AD2, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.116A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.425A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.459A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.906A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 14 removed outlier: 4.675A pdb=" N GLY K 100 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER I 96 " --> pdb=" O VAL I 100H" (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL I 100H" --> pdb=" O SER I 96 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AE3, first strand: chain 'D' and resid 45 through 47 removed outlier: 7.466A pdb=" N VAL D 242 " --> pdb=" O HIS D 85 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N HIS D 85 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AE5, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE6, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AE7, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AE8, first strand: chain 'D' and resid 158 through 162 Processing sheet with id=AE9, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.117A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.425A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.460A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.906A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 1989 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: 3.57 Time building geometry restraints manager: 2.52 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: 4876 1.32 - 1.46: 6261 1.46 - 1.60: 8579 1.60 - 1.73: 15 1.73 - 1.87: 159 Bond restraints: 19890 Sorted by residual: bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C1 NAG e 2 " pdb=" O5 NAG e 2 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 19885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 23410 2.54 - 5.09: 3048 5.09 - 7.63: 515 7.63 - 10.17: 26 10.17 - 12.71: 10 Bond angle restraints: 27009 Sorted by residual: angle pdb=" N SER J 90 " pdb=" CA SER J 90 " pdb=" C SER J 90 " ideal model delta sigma weight residual 111.07 121.28 -10.21 1.07e+00 8.73e-01 9.11e+01 angle pdb=" N SER K 90 " pdb=" CA SER K 90 " pdb=" C SER K 90 " ideal model delta sigma weight residual 111.07 121.27 -10.20 1.07e+00 8.73e-01 9.09e+01 angle pdb=" N SER L 90 " pdb=" CA SER L 90 " pdb=" C SER L 90 " ideal model delta sigma weight residual 111.07 121.25 -10.18 1.07e+00 8.73e-01 9.04e+01 angle pdb=" C ILE I 48 " pdb=" CA ILE I 48 " pdb=" CB ILE I 48 " ideal model delta sigma weight residual 111.71 104.26 7.45 8.50e-01 1.38e+00 7.67e+01 angle pdb=" C ILE G 48 " pdb=" CA ILE G 48 " pdb=" CB ILE G 48 " ideal model delta sigma weight residual 111.71 104.27 7.44 8.50e-01 1.38e+00 7.65e+01 ... (remaining 27004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 12321 21.52 - 43.04: 363 43.04 - 64.55: 99 64.55 - 86.07: 30 86.07 - 107.59: 12 Dihedral angle restraints: 12825 sinusoidal: 6039 harmonic: 6786 Sorted by residual: dihedral pdb=" O4 BMA c 3 " pdb=" C4 BMA c 3 " pdb=" C5 BMA c 3 " pdb=" O5 BMA c 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.88 107.59 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" O4 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C5 BMA O 3 " pdb=" O5 BMA O 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.84 107.55 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" O4 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C5 BMA V 3 " pdb=" O5 BMA V 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.83 107.54 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 12822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2230 0.098 - 0.195: 810 0.195 - 0.293: 182 0.293 - 0.390: 18 0.390 - 0.488: 3 Chirality restraints: 3243 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.84e+01 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.82e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.81e+01 ... (remaining 3240 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 109 " 0.047 2.00e-02 2.50e+03 9.68e-02 9.37e+01 pdb=" C VAL H 109 " -0.167 2.00e-02 2.50e+03 pdb=" O VAL H 109 " 0.062 2.00e-02 2.50e+03 pdb=" OXT VAL H 109 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 109 " -0.047 2.00e-02 2.50e+03 9.67e-02 9.36e+01 pdb=" C VAL G 109 " 0.167 2.00e-02 2.50e+03 pdb=" O VAL G 109 " -0.062 2.00e-02 2.50e+03 pdb=" OXT VAL G 109 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 109 " 0.047 2.00e-02 2.50e+03 9.67e-02 9.35e+01 pdb=" C VAL I 109 " -0.167 2.00e-02 2.50e+03 pdb=" O VAL I 109 " 0.062 2.00e-02 2.50e+03 pdb=" OXT VAL I 109 " 0.058 2.00e-02 2.50e+03 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 8036 2.88 - 3.39: 17290 3.39 - 3.89: 33084 3.89 - 4.40: 37992 4.40 - 4.90: 61141 Nonbonded interactions: 157543 Sorted by model distance: nonbonded pdb=" OG1 THR H 72 " pdb=" OG1 THR H 76 " model vdw 2.380 3.040 nonbonded pdb=" OG1 THR I 72 " pdb=" OG1 THR I 76 " model vdw 2.380 3.040 nonbonded pdb=" OG1 THR G 72 " pdb=" OG1 THR G 76 " model vdw 2.380 3.040 nonbonded pdb=" OD2 ASP A 57 " pdb=" NZ LYS A 59 " model vdw 2.404 3.120 nonbonded pdb=" OD2 ASP D 57 " pdb=" NZ LYS D 59 " model vdw 2.405 3.120 ... (remaining 157538 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.750 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.022 0.147 20004 Z= 1.161 Angle : 1.824 12.713 27309 Z= 1.184 Chirality : 0.104 0.488 3243 Planarity : 0.010 0.097 3339 Dihedral : 11.748 107.590 8331 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.78 % Allowed : 3.64 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.22 (0.17), residues: 2310 helix: -0.48 (0.23), residues: 447 sheet: 0.49 (0.18), residues: 708 loop : 0.36 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 95C TYR 0.067 0.008 TYR B 638 PHE 0.027 0.005 PHE A 53 TRP 0.061 0.010 TRP J 35 HIS 0.013 0.003 HIS H 100F Details of bonding type rmsd covalent geometry : bond 0.02186 (19890) covalent geometry : angle 1.79611 (27009) SS BOND : bond 0.02012 ( 42) SS BOND : angle 3.63762 ( 84) hydrogen bonds : bond 0.17194 ( 741) hydrogen bonds : angle 7.82075 ( 1989) link_BETA1-4 : bond 0.02845 ( 24) link_BETA1-4 : angle 3.79808 ( 72) link_NAG-ASN : bond 0.03088 ( 48) link_NAG-ASN : angle 3.31612 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 62 PHE cc_start: 0.8541 (m-80) cc_final: 0.8228 (m-80) REVERT: H 82 LEU cc_start: 0.8814 (mt) cc_final: 0.8563 (mp) REVERT: A 481 SER cc_start: 0.8662 (p) cc_final: 0.8400 (t) REVERT: B 543 ASN cc_start: 0.8300 (t0) cc_final: 0.8087 (t0) REVERT: G 82 LEU cc_start: 0.8803 (mt) cc_final: 0.8548 (mp) REVERT: C 481 SER cc_start: 0.8745 (p) cc_final: 0.8510 (t) REVERT: E 658 GLN cc_start: 0.7587 (tt0) cc_final: 0.7349 (tm-30) REVERT: K 39 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8189 (mmmm) REVERT: K 73 LEU cc_start: 0.8841 (mt) cc_final: 0.8533 (tp) REVERT: D 180 ASP cc_start: 0.7790 (m-30) cc_final: 0.7527 (m-30) REVERT: D 481 SER cc_start: 0.8680 (p) cc_final: 0.8445 (t) REVERT: F 543 ASN cc_start: 0.8246 (t0) cc_final: 0.7995 (t0) REVERT: F 658 GLN cc_start: 0.7644 (tt0) cc_final: 0.7331 (tm-30) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.1509 time to fit residues: 120.5629 Evaluate side-chains 266 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 89 GLN L 91 ASN H 39 GLN H 100FHIS A 72 HIS A 195 ASN A 216 HIS A 374 HIS A 478 ASN B 625 ASN B 653 GLN J 38 GLN J 42 GLN J 89 GLN J 91 ASN G 100FHIS C 72 HIS C 94 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 216 HIS C 300 ASN E 625 ASN E 653 GLN K 38 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 100FHIS D 72 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN D 216 HIS D 352 HIS F 591 GLN F 625 ASN F 653 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.089543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070983 restraints weight = 57726.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073531 restraints weight = 29158.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.075142 restraints weight = 19538.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.076131 restraints weight = 15310.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.076729 restraints weight = 13194.675| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20004 Z= 0.189 Angle : 0.828 9.754 27309 Z= 0.428 Chirality : 0.048 0.226 3243 Planarity : 0.005 0.048 3339 Dihedral : 8.333 59.369 4035 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.94 % Favored : 95.54 % Rotamer: Outliers : 2.34 % Allowed : 9.49 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.17), residues: 2310 helix: 0.70 (0.26), residues: 417 sheet: 0.24 (0.18), residues: 699 loop : -0.50 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 66 TYR 0.025 0.002 TYR H 100C PHE 0.016 0.002 PHE I 98 TRP 0.021 0.002 TRP E 614 HIS 0.008 0.001 HIS I 100F Details of bonding type rmsd covalent geometry : bond 0.00411 (19890) covalent geometry : angle 0.79881 (27009) SS BOND : bond 0.00383 ( 42) SS BOND : angle 1.22404 ( 84) hydrogen bonds : bond 0.06138 ( 741) hydrogen bonds : angle 6.01919 ( 1989) link_BETA1-4 : bond 0.00501 ( 24) link_BETA1-4 : angle 2.48449 ( 72) link_NAG-ASN : bond 0.00579 ( 48) link_NAG-ASN : angle 2.52202 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 361 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 GLN cc_start: 0.8431 (tp40) cc_final: 0.8221 (tp40) REVERT: L 94 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8808 (mt) REVERT: L 107 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7034 (tptt) REVERT: A 150 MET cc_start: 0.8454 (tpt) cc_final: 0.8216 (tpp) REVERT: A 243 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8123 (t) REVERT: B 543 ASN cc_start: 0.8621 (t0) cc_final: 0.8112 (t0) REVERT: G 5 VAL cc_start: 0.8761 (t) cc_final: 0.8553 (t) REVERT: G 38 ARG cc_start: 0.8406 (ptt180) cc_final: 0.8095 (ptt180) REVERT: G 39 GLN cc_start: 0.8311 (tt0) cc_final: 0.7877 (tt0) REVERT: G 86 ASP cc_start: 0.8342 (m-30) cc_final: 0.8106 (m-30) REVERT: E 543 ASN cc_start: 0.8257 (t0) cc_final: 0.7939 (t0) REVERT: K 4 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6737 (mtp) REVERT: I 4 LEU cc_start: 0.8737 (mm) cc_final: 0.8537 (mm) REVERT: I 82 LEU cc_start: 0.9043 (mt) cc_final: 0.8647 (mp) REVERT: D 99 ASN cc_start: 0.8355 (p0) cc_final: 0.8104 (t0) REVERT: D 150 MET cc_start: 0.8780 (tpp) cc_final: 0.8330 (tpp) REVERT: D 180 ASP cc_start: 0.8015 (m-30) cc_final: 0.7769 (m-30) REVERT: D 243 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8267 (t) REVERT: D 434 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7631 (ttp) REVERT: F 543 ASN cc_start: 0.8642 (t0) cc_final: 0.8129 (t0) REVERT: F 601 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7962 (ptmt) REVERT: F 659 ASP cc_start: 0.8706 (m-30) cc_final: 0.8421 (m-30) outliers start: 48 outliers final: 21 residues processed: 385 average time/residue: 0.1254 time to fit residues: 76.2719 Evaluate side-chains 292 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 612 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 158 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 91 ASN A 105 HIS A 352 HIS B 625 ASN B 653 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 352 HIS C 478 ASN K 42 GLN I 39 GLN D 105 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN F 625 ASN F 653 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.083021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.062516 restraints weight = 58957.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065037 restraints weight = 29806.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.066646 restraints weight = 20196.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067648 restraints weight = 15965.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068285 restraints weight = 13827.211| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 20004 Z= 0.284 Angle : 0.806 8.567 27309 Z= 0.415 Chirality : 0.050 0.242 3243 Planarity : 0.005 0.051 3339 Dihedral : 7.541 53.084 4035 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.45 % Favored : 94.03 % Rotamer: Outliers : 3.36 % Allowed : 11.58 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.51 (0.17), residues: 2310 helix: 0.68 (0.26), residues: 417 sheet: 0.01 (0.18), residues: 726 loop : -0.90 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 429 TYR 0.022 0.002 TYR E 586 PHE 0.021 0.003 PHE G 98 TRP 0.023 0.002 TRP C 96 HIS 0.007 0.002 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00658 (19890) covalent geometry : angle 0.78103 (27009) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.22692 ( 84) hydrogen bonds : bond 0.05596 ( 741) hydrogen bonds : angle 5.74752 ( 1989) link_BETA1-4 : bond 0.00412 ( 24) link_BETA1-4 : angle 2.03934 ( 72) link_NAG-ASN : bond 0.00613 ( 48) link_NAG-ASN : angle 2.38752 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8668 (mm) cc_final: 0.8279 (mm) REVERT: H 53 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8734 (t0) REVERT: H 80 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7542 (tpp80) REVERT: A 150 MET cc_start: 0.8647 (tpt) cc_final: 0.8291 (tpp) REVERT: A 234 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6786 (t0) REVERT: A 243 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8047 (t) REVERT: A 271 MET cc_start: 0.8015 (tpp) cc_final: 0.7343 (tpp) REVERT: B 543 ASN cc_start: 0.8973 (t0) cc_final: 0.8282 (t0) REVERT: B 624 ASP cc_start: 0.8180 (t0) cc_final: 0.7517 (p0) REVERT: J 4 MET cc_start: 0.7607 (mtp) cc_final: 0.6796 (mtm) REVERT: J 77 ASP cc_start: 0.8992 (t0) cc_final: 0.8496 (t0) REVERT: G 4 LEU cc_start: 0.8613 (mm) cc_final: 0.8152 (mm) REVERT: G 80 ARG cc_start: 0.8019 (tpp80) cc_final: 0.7699 (tpp80) REVERT: E 543 ASN cc_start: 0.8640 (t0) cc_final: 0.8160 (t0) REVERT: K 38 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: I 4 LEU cc_start: 0.8658 (mm) cc_final: 0.8412 (mm) REVERT: I 39 GLN cc_start: 0.8944 (tt0) cc_final: 0.8159 (tt0) REVERT: D 234 ASN cc_start: 0.7062 (OUTLIER) cc_final: 0.6669 (t0) REVERT: D 243 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8089 (t) REVERT: F 543 ASN cc_start: 0.8991 (t0) cc_final: 0.8362 (t0) REVERT: F 624 ASP cc_start: 0.8495 (t0) cc_final: 0.7681 (p0) REVERT: F 626 MET cc_start: 0.7173 (mmt) cc_final: 0.6773 (tpp) outliers start: 69 outliers final: 34 residues processed: 307 average time/residue: 0.1301 time to fit residues: 62.6728 Evaluate side-chains 280 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 240 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 71 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.083458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.063096 restraints weight = 58713.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065631 restraints weight = 29477.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.067257 restraints weight = 19862.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.068234 restraints weight = 15645.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068880 restraints weight = 13575.405| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 20004 Z= 0.201 Angle : 0.709 9.351 27309 Z= 0.363 Chirality : 0.046 0.250 3243 Planarity : 0.004 0.050 3339 Dihedral : 6.792 49.787 4035 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.28 % Favored : 94.20 % Rotamer: Outliers : 2.92 % Allowed : 12.41 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.56 (0.17), residues: 2310 helix: 0.77 (0.26), residues: 417 sheet: 0.01 (0.19), residues: 705 loop : -1.00 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 429 TYR 0.022 0.002 TYR E 586 PHE 0.021 0.002 PHE J 98 TRP 0.015 0.002 TRP E 628 HIS 0.004 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00462 (19890) covalent geometry : angle 0.68841 (27009) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.09612 ( 84) hydrogen bonds : bond 0.05001 ( 741) hydrogen bonds : angle 5.53093 ( 1989) link_BETA1-4 : bond 0.00463 ( 24) link_BETA1-4 : angle 1.72537 ( 72) link_NAG-ASN : bond 0.00464 ( 48) link_NAG-ASN : angle 2.08989 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 ASN cc_start: 0.9035 (m-40) cc_final: 0.8820 (m-40) REVERT: H 53 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8771 (t0) REVERT: H 54 ASP cc_start: 0.8751 (p0) cc_final: 0.8541 (p0) REVERT: H 80 ARG cc_start: 0.8033 (tpp80) cc_final: 0.7687 (tpp80) REVERT: A 150 MET cc_start: 0.8542 (tpt) cc_final: 0.8241 (tpp) REVERT: A 243 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8060 (t) REVERT: B 543 ASN cc_start: 0.8978 (t0) cc_final: 0.8279 (t0) REVERT: B 624 ASP cc_start: 0.8118 (t0) cc_final: 0.7518 (p0) REVERT: J 4 MET cc_start: 0.7444 (mtp) cc_final: 0.6678 (mtp) REVERT: J 42 GLN cc_start: 0.8521 (mp10) cc_final: 0.7957 (mp10) REVERT: G 4 LEU cc_start: 0.8634 (mm) cc_final: 0.8257 (mm) REVERT: G 39 GLN cc_start: 0.8642 (tt0) cc_final: 0.7767 (tt0) REVERT: G 45 LEU cc_start: 0.9201 (mt) cc_final: 0.8873 (mt) REVERT: G 80 ARG cc_start: 0.8075 (tpp80) cc_final: 0.7799 (tpp80) REVERT: G 82 LEU cc_start: 0.8520 (mm) cc_final: 0.8117 (tt) REVERT: E 543 ASN cc_start: 0.8766 (t0) cc_final: 0.8166 (t0) REVERT: K 38 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: I 4 LEU cc_start: 0.8761 (mm) cc_final: 0.8533 (mm) REVERT: I 39 GLN cc_start: 0.8844 (tt0) cc_final: 0.8083 (tt0) REVERT: I 80 ARG cc_start: 0.8023 (tpp80) cc_final: 0.7786 (tpp80) REVERT: F 543 ASN cc_start: 0.9062 (t0) cc_final: 0.8412 (t0) REVERT: F 624 ASP cc_start: 0.8378 (t0) cc_final: 0.7718 (p0) outliers start: 60 outliers final: 40 residues processed: 292 average time/residue: 0.1258 time to fit residues: 58.4919 Evaluate side-chains 285 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 156 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN H 39 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.081988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.062488 restraints weight = 58955.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.064751 restraints weight = 31774.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066182 restraints weight = 22235.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067071 restraints weight = 17946.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067612 restraints weight = 15725.836| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 20004 Z= 0.287 Angle : 0.773 9.088 27309 Z= 0.392 Chirality : 0.049 0.278 3243 Planarity : 0.005 0.055 3339 Dihedral : 7.044 57.187 4035 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.06 % Favored : 93.55 % Rotamer: Outliers : 4.18 % Allowed : 12.36 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.81 (0.17), residues: 2310 helix: 0.96 (0.27), residues: 396 sheet: -0.21 (0.19), residues: 690 loop : -1.23 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 166 TYR 0.023 0.002 TYR E 586 PHE 0.022 0.002 PHE G 98 TRP 0.018 0.002 TRP E 628 HIS 0.006 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00665 (19890) covalent geometry : angle 0.75039 (27009) SS BOND : bond 0.00439 ( 42) SS BOND : angle 1.15001 ( 84) hydrogen bonds : bond 0.05227 ( 741) hydrogen bonds : angle 5.58119 ( 1989) link_BETA1-4 : bond 0.00403 ( 24) link_BETA1-4 : angle 1.71462 ( 72) link_NAG-ASN : bond 0.00601 ( 48) link_NAG-ASN : angle 2.33108 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 254 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 77 ASP cc_start: 0.8649 (t0) cc_final: 0.8236 (t0) REVERT: H 53 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8573 (t0) REVERT: A 271 MET cc_start: 0.8034 (tpp) cc_final: 0.7420 (tpp) REVERT: B 543 ASN cc_start: 0.8549 (t0) cc_final: 0.8013 (t0) REVERT: J 4 MET cc_start: 0.7301 (mtp) cc_final: 0.6967 (mtp) REVERT: J 94 LEU cc_start: 0.9023 (mm) cc_final: 0.8719 (mt) REVERT: J 103 GLU cc_start: 0.8301 (tp30) cc_final: 0.8030 (tp30) REVERT: G 82 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8354 (tt) REVERT: E 543 ASN cc_start: 0.8458 (t0) cc_final: 0.8053 (t0) REVERT: E 624 ASP cc_start: 0.8006 (t0) cc_final: 0.7630 (p0) REVERT: K 38 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: K 77 ASP cc_start: 0.8725 (t0) cc_final: 0.8473 (t0) REVERT: I 39 GLN cc_start: 0.8795 (tt0) cc_final: 0.8246 (tt0) REVERT: I 53 ASP cc_start: 0.8770 (m-30) cc_final: 0.8514 (t0) REVERT: D 271 MET cc_start: 0.7643 (tpt) cc_final: 0.7225 (tpp) REVERT: F 543 ASN cc_start: 0.8640 (t0) cc_final: 0.8226 (t0) REVERT: F 624 ASP cc_start: 0.7801 (t0) cc_final: 0.7585 (p0) outliers start: 86 outliers final: 57 residues processed: 313 average time/residue: 0.1247 time to fit residues: 62.0600 Evaluate side-chains 289 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 165 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN J 6 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.082070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.062544 restraints weight = 58328.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064811 restraints weight = 31197.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066278 restraints weight = 21633.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067170 restraints weight = 17349.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067732 restraints weight = 15181.341| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 20004 Z= 0.251 Angle : 0.755 10.962 27309 Z= 0.382 Chirality : 0.048 0.278 3243 Planarity : 0.005 0.054 3339 Dihedral : 6.872 54.902 4035 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.93 % Favored : 93.68 % Rotamer: Outliers : 3.65 % Allowed : 13.77 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.92 (0.17), residues: 2310 helix: 0.89 (0.27), residues: 399 sheet: -0.30 (0.19), residues: 708 loop : -1.32 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 166 TYR 0.015 0.002 TYR G 100C PHE 0.020 0.002 PHE G 98 TRP 0.017 0.001 TRP E 628 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00585 (19890) covalent geometry : angle 0.73264 (27009) SS BOND : bond 0.00411 ( 42) SS BOND : angle 1.46382 ( 84) hydrogen bonds : bond 0.04972 ( 741) hydrogen bonds : angle 5.49990 ( 1989) link_BETA1-4 : bond 0.00407 ( 24) link_BETA1-4 : angle 1.56499 ( 72) link_NAG-ASN : bond 0.00547 ( 48) link_NAG-ASN : angle 2.20542 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 243 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 53 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8593 (t0) REVERT: A 243 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8275 (t) REVERT: A 271 MET cc_start: 0.7925 (tpp) cc_final: 0.7388 (tpp) REVERT: B 543 ASN cc_start: 0.8562 (t0) cc_final: 0.8021 (t0) REVERT: J 42 GLN cc_start: 0.8368 (mp10) cc_final: 0.8139 (mp10) REVERT: J 103 GLU cc_start: 0.8280 (tp30) cc_final: 0.8010 (tp30) REVERT: G 82 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8336 (tt) REVERT: G 86 ASP cc_start: 0.8525 (m-30) cc_final: 0.8213 (m-30) REVERT: E 540 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7069 (mp10) REVERT: E 543 ASN cc_start: 0.8498 (t0) cc_final: 0.8131 (t0) REVERT: E 624 ASP cc_start: 0.7853 (t0) cc_final: 0.7598 (p0) REVERT: K 38 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: I 39 GLN cc_start: 0.8785 (tt0) cc_final: 0.8206 (tt0) REVERT: I 53 ASP cc_start: 0.8767 (m-30) cc_final: 0.8522 (t0) REVERT: D 271 MET cc_start: 0.7638 (tpt) cc_final: 0.7171 (tpp) REVERT: F 543 ASN cc_start: 0.8709 (t0) cc_final: 0.8257 (t0) outliers start: 75 outliers final: 57 residues processed: 291 average time/residue: 0.1243 time to fit residues: 58.2427 Evaluate side-chains 294 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 232 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 41 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064106 restraints weight = 58451.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.066436 restraints weight = 30801.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.067939 restraints weight = 21276.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.068843 restraints weight = 17023.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069368 restraints weight = 14854.072| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20004 Z= 0.162 Angle : 0.695 11.524 27309 Z= 0.353 Chirality : 0.046 0.274 3243 Planarity : 0.004 0.053 3339 Dihedral : 6.382 43.238 4035 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.84 % Favored : 93.77 % Rotamer: Outliers : 3.11 % Allowed : 14.79 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.89 (0.17), residues: 2310 helix: 0.98 (0.26), residues: 408 sheet: -0.28 (0.19), residues: 735 loop : -1.37 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 166 TYR 0.016 0.001 TYR G 100C PHE 0.018 0.002 PHE G 98 TRP 0.019 0.001 TRP B 631 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00371 (19890) covalent geometry : angle 0.67584 (27009) SS BOND : bond 0.00381 ( 42) SS BOND : angle 1.40147 ( 84) hydrogen bonds : bond 0.04480 ( 741) hydrogen bonds : angle 5.33426 ( 1989) link_BETA1-4 : bond 0.00457 ( 24) link_BETA1-4 : angle 1.41309 ( 72) link_NAG-ASN : bond 0.00436 ( 48) link_NAG-ASN : angle 1.97249 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 253 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ARG cc_start: 0.8083 (ptm-80) cc_final: 0.7829 (ptm-80) REVERT: H 53 ASP cc_start: 0.8840 (m-30) cc_final: 0.8622 (t0) REVERT: A 271 MET cc_start: 0.7844 (tpp) cc_final: 0.7227 (tpp) REVERT: B 530 MET cc_start: 0.8188 (mmm) cc_final: 0.7894 (mmm) REVERT: B 543 ASN cc_start: 0.8565 (t0) cc_final: 0.8144 (t0) REVERT: J 103 GLU cc_start: 0.8310 (tp30) cc_final: 0.8048 (tp30) REVERT: G 82 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8337 (tt) REVERT: G 86 ASP cc_start: 0.8510 (m-30) cc_final: 0.8290 (m-30) REVERT: C 150 MET cc_start: 0.8277 (tpp) cc_final: 0.7917 (tpp) REVERT: E 543 ASN cc_start: 0.8513 (t0) cc_final: 0.8145 (t0) REVERT: K 38 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8257 (tp40) REVERT: I 53 ASP cc_start: 0.8768 (m-30) cc_final: 0.8516 (t0) REVERT: D 243 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8220 (t) REVERT: D 271 MET cc_start: 0.7605 (tpt) cc_final: 0.7114 (tpp) REVERT: F 543 ASN cc_start: 0.8733 (t0) cc_final: 0.8276 (t0) outliers start: 64 outliers final: 46 residues processed: 292 average time/residue: 0.1240 time to fit residues: 57.4254 Evaluate side-chains 285 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 53 optimal weight: 0.0370 chunk 213 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 198 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 103 GLN C 103 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 103 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.085228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065954 restraints weight = 57886.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068309 restraints weight = 30682.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.069802 restraints weight = 21165.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.070705 restraints weight = 16903.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.071216 restraints weight = 14771.864| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20004 Z= 0.125 Angle : 0.666 11.834 27309 Z= 0.339 Chirality : 0.045 0.268 3243 Planarity : 0.004 0.055 3339 Dihedral : 5.929 40.403 4035 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.76 % Favored : 93.85 % Rotamer: Outliers : 2.73 % Allowed : 15.52 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.85 (0.17), residues: 2310 helix: 0.93 (0.26), residues: 426 sheet: -0.18 (0.19), residues: 675 loop : -1.36 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 166 TYR 0.018 0.001 TYR G 100C PHE 0.016 0.001 PHE G 98 TRP 0.035 0.001 TRP E 631 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00276 (19890) covalent geometry : angle 0.64926 (27009) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.29143 ( 84) hydrogen bonds : bond 0.04117 ( 741) hydrogen bonds : angle 5.18418 ( 1989) link_BETA1-4 : bond 0.00492 ( 24) link_BETA1-4 : angle 1.32186 ( 72) link_NAG-ASN : bond 0.00415 ( 48) link_NAG-ASN : angle 1.81089 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ARG cc_start: 0.8108 (ptm-80) cc_final: 0.7874 (ptm-80) REVERT: A 271 MET cc_start: 0.7757 (tpp) cc_final: 0.7141 (tpp) REVERT: B 543 ASN cc_start: 0.8529 (t0) cc_final: 0.8140 (t0) REVERT: J 21 ILE cc_start: 0.9134 (mt) cc_final: 0.8841 (mm) REVERT: J 103 GLU cc_start: 0.8187 (tp30) cc_final: 0.7912 (tp30) REVERT: E 543 ASN cc_start: 0.8496 (t0) cc_final: 0.8150 (t0) REVERT: K 38 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8169 (tp40) REVERT: I 5 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8744 (m) REVERT: I 53 ASP cc_start: 0.8684 (m-30) cc_final: 0.8429 (t0) REVERT: D 243 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8178 (t) REVERT: D 271 MET cc_start: 0.7526 (tpt) cc_final: 0.7074 (tpp) REVERT: F 543 ASN cc_start: 0.8637 (t0) cc_final: 0.8240 (t0) outliers start: 56 outliers final: 41 residues processed: 302 average time/residue: 0.1288 time to fit residues: 61.4289 Evaluate side-chains 285 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 207 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 147 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.063080 restraints weight = 58124.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065298 restraints weight = 31499.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.066709 restraints weight = 22067.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.067563 restraints weight = 17826.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.068128 restraints weight = 15658.892| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20004 Z= 0.249 Angle : 0.752 14.522 27309 Z= 0.380 Chirality : 0.048 0.289 3243 Planarity : 0.005 0.058 3339 Dihedral : 6.304 42.735 4035 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.67 % Favored : 92.86 % Rotamer: Outliers : 2.58 % Allowed : 16.45 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.89 (0.17), residues: 2310 helix: 1.08 (0.26), residues: 405 sheet: -0.23 (0.19), residues: 711 loop : -1.43 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 166 TYR 0.017 0.002 TYR E 586 PHE 0.018 0.002 PHE G 98 TRP 0.029 0.002 TRP E 631 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00585 (19890) covalent geometry : angle 0.73266 (27009) SS BOND : bond 0.00447 ( 42) SS BOND : angle 1.31954 ( 84) hydrogen bonds : bond 0.04659 ( 741) hydrogen bonds : angle 5.34263 ( 1989) link_BETA1-4 : bond 0.00384 ( 24) link_BETA1-4 : angle 1.49792 ( 72) link_NAG-ASN : bond 0.00503 ( 48) link_NAG-ASN : angle 2.07256 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ARG cc_start: 0.8205 (ptm-80) cc_final: 0.7979 (ptm-80) REVERT: A 243 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8266 (t) REVERT: A 271 MET cc_start: 0.7855 (tpp) cc_final: 0.7288 (tpp) REVERT: B 543 ASN cc_start: 0.8640 (t0) cc_final: 0.8215 (t0) REVERT: J 21 ILE cc_start: 0.9152 (mt) cc_final: 0.8875 (mm) REVERT: J 103 GLU cc_start: 0.8211 (tp30) cc_final: 0.7927 (tp30) REVERT: C 271 MET cc_start: 0.7882 (tpp) cc_final: 0.7495 (tpp) REVERT: E 543 ASN cc_start: 0.8631 (t0) cc_final: 0.8246 (t0) REVERT: K 38 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8185 (tp40) REVERT: I 53 ASP cc_start: 0.8794 (m-30) cc_final: 0.8551 (t0) REVERT: D 271 MET cc_start: 0.7596 (tpt) cc_final: 0.7130 (tpp) REVERT: F 543 ASN cc_start: 0.8749 (t0) cc_final: 0.8289 (t0) outliers start: 53 outliers final: 47 residues processed: 278 average time/residue: 0.1215 time to fit residues: 54.3424 Evaluate side-chains 284 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 225 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 0.0170 chunk 39 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 224 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.085645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.066308 restraints weight = 58438.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.068664 restraints weight = 31057.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.070156 restraints weight = 21451.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.071087 restraints weight = 17171.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.071670 restraints weight = 14967.903| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20004 Z= 0.127 Angle : 0.686 11.319 27309 Z= 0.348 Chirality : 0.045 0.258 3243 Planarity : 0.004 0.058 3339 Dihedral : 5.859 39.095 4035 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.54 % Favored : 93.98 % Rotamer: Outliers : 2.34 % Allowed : 16.79 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.86 (0.17), residues: 2310 helix: 0.98 (0.26), residues: 426 sheet: -0.12 (0.19), residues: 705 loop : -1.46 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 166 TYR 0.018 0.001 TYR I 100C PHE 0.017 0.001 PHE G 98 TRP 0.045 0.001 TRP E 631 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00282 (19890) covalent geometry : angle 0.67085 (27009) SS BOND : bond 0.00244 ( 42) SS BOND : angle 1.24195 ( 84) hydrogen bonds : bond 0.04150 ( 741) hydrogen bonds : angle 5.13330 ( 1989) link_BETA1-4 : bond 0.00526 ( 24) link_BETA1-4 : angle 1.28775 ( 72) link_NAG-ASN : bond 0.00415 ( 48) link_NAG-ASN : angle 1.75340 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.7823 (tpp) cc_final: 0.7177 (tpp) REVERT: B 543 ASN cc_start: 0.8617 (t0) cc_final: 0.8278 (t0) REVERT: J 4 MET cc_start: 0.7613 (mmm) cc_final: 0.7391 (mmm) REVERT: J 21 ILE cc_start: 0.9014 (mt) cc_final: 0.8760 (mm) REVERT: J 103 GLU cc_start: 0.8143 (tp30) cc_final: 0.7922 (tp30) REVERT: C 150 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7778 (mmm) REVERT: E 543 ASN cc_start: 0.8622 (t0) cc_final: 0.8237 (t0) REVERT: E 626 MET cc_start: 0.6664 (tpp) cc_final: 0.6348 (tpp) REVERT: K 38 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8165 (tp40) REVERT: I 53 ASP cc_start: 0.8716 (m-30) cc_final: 0.8477 (t0) REVERT: D 243 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8261 (t) REVERT: D 271 MET cc_start: 0.7586 (tpt) cc_final: 0.7073 (tpp) REVERT: F 543 ASN cc_start: 0.8726 (t0) cc_final: 0.8301 (t0) outliers start: 48 outliers final: 40 residues processed: 289 average time/residue: 0.1251 time to fit residues: 57.6892 Evaluate side-chains 286 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 83 optimal weight: 0.0980 chunk 228 optimal weight: 7.9990 chunk 213 optimal weight: 0.4980 chunk 182 optimal weight: 6.9990 chunk 35 optimal weight: 0.0870 chunk 202 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN H 39 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.083539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.063187 restraints weight = 58394.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.065761 restraints weight = 28367.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067407 restraints weight = 18715.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.068440 restraints weight = 14586.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068949 restraints weight = 12513.449| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20004 Z= 0.152 Angle : 0.690 12.306 27309 Z= 0.350 Chirality : 0.045 0.271 3243 Planarity : 0.004 0.059 3339 Dihedral : 5.802 39.874 4035 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.19 % Favored : 93.25 % Rotamer: Outliers : 2.29 % Allowed : 17.62 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.73 (0.17), residues: 2310 helix: 1.39 (0.26), residues: 405 sheet: -0.11 (0.19), residues: 714 loop : -1.41 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 166 TYR 0.017 0.001 TYR H 100C PHE 0.016 0.002 PHE G 98 TRP 0.038 0.001 TRP F 631 HIS 0.002 0.001 HIS K 27 Details of bonding type rmsd covalent geometry : bond 0.00350 (19890) covalent geometry : angle 0.67442 (27009) SS BOND : bond 0.00322 ( 42) SS BOND : angle 1.20506 ( 84) hydrogen bonds : bond 0.04194 ( 741) hydrogen bonds : angle 5.13212 ( 1989) link_BETA1-4 : bond 0.00405 ( 24) link_BETA1-4 : angle 1.34901 ( 72) link_NAG-ASN : bond 0.00368 ( 48) link_NAG-ASN : angle 1.81197 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.39 seconds wall clock time: 59 minutes 36.81 seconds (3576.81 seconds total)