Starting phenix.real_space_refine on Sat Jun 6 01:19:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p6g_71308/06_2026/9p6g_71308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p6g_71308/06_2026/9p6g_71308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p6g_71308/06_2026/9p6g_71308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p6g_71308/06_2026/9p6g_71308.map" model { file = "/net/cci-nas-00/data/ceres_data/9p6g_71308/06_2026/9p6g_71308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p6g_71308/06_2026/9p6g_71308.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 15507 2.51 5 N 4167 2.21 5 O 4869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24684 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3415 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 4 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 928 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1085 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "L" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 717 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "C" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3415 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 4 Chain: "D" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "J" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 928 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "K" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1085 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "N" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 717 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "E" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3415 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 4 Chain: "F" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "O" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 928 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "P" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1085 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "R" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 717 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "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 Time building chain proxies: 6.57, per 1000 atoms: 0.27 Number of scatterers: 24684 At special positions: 0 Unit cell: (138.543, 142.678, 146.814, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 4869 8.00 N 4167 7.00 C 15507 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " 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 ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA W 3 " - " MAN W 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 88 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 295 " " NAG A 607 " - " ASN A 156 " " NAG A 608 " - " ASN A 197 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 234 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 88 " " NAG C 605 " - " ASN C 332 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 156 " " NAG C 608 " - " ASN C 197 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 234 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 88 " " NAG E 605 " - " ASN E 332 " " NAG E 606 " - " ASN E 295 " " NAG E 607 " - " ASN E 156 " " NAG E 608 " - " ASN E 197 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 234 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG S 1 " - " ASN A 276 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 262 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 392 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN E 276 " " NAG b 1 " - " ASN E 386 " " NAG c 1 " - " ASN E 392 " " NAG d 1 " - " ASN E 262 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.4 seconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5532 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 45 sheets defined 15.7% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 98 through 114 removed outlier: 3.790A 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 335 through 354 removed outlier: 3.590A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.708A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.630A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.515A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 114 removed outlier: 3.790A 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 335 through 354 removed outlier: 3.590A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.708A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.630A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.516A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 114 removed outlier: 3.790A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.590A pdb=" N GLN E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 480 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.708A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 removed outlier: 3.630A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 28 through 30 No H-bonds generated for 'chain 'P' and resid 28 through 30' Processing helix chain 'P' and resid 60 through 64 Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.514A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.340A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.746A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.033A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 6.453A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'G' and resid 34 through 39 removed outlier: 6.979A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'I' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 9 through 11 current: chain 'I' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 45 through 48 current: chain 'I' and resid 96 through 98 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.643A pdb=" N GLY H 76G" --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 58 current: chain 'H' and resid 100K through 103 Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.663A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.341A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.746A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.033A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 308 removed outlier: 6.453A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 316 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'J' and resid 34 through 39 removed outlier: 6.980A pdb=" N MET J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC7, first strand: chain 'M' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 9 through 11 current: chain 'M' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 96 through 98 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.643A pdb=" N GLY K 76G" --> pdb=" O ALA K 24 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 58 current: chain 'K' and resid 100K through 103 Processing sheet with id=AD2, first strand: chain 'N' and resid 9 through 11 removed outlier: 6.663A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 18 through 24 Processing sheet with id=AD4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.340A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.747A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.033A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 308 removed outlier: 6.454A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 316 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AE2, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'O' and resid 34 through 39 removed outlier: 6.979A pdb=" N MET O 34 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100H through 103 Processing sheet with id=AE4, first strand: chain 'Q' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 9 through 11 current: chain 'Q' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 45 through 48 current: chain 'Q' and resid 96 through 98 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AE6, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.643A pdb=" N GLY P 76G" --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 10 through 12 current: chain 'P' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 58 current: chain 'P' and resid 100K through 103 Processing sheet with id=AE8, first strand: chain 'R' and resid 9 through 11 removed outlier: 6.662A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 18 through 24 663 hydrogen bonds defined for protein. 1764 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: 5.24 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7836 1.35 - 1.48: 6808 1.48 - 1.61: 10382 1.61 - 1.75: 0 1.75 - 1.88: 192 Bond restraints: 25218 Sorted by residual: bond pdb=" CB CYS E 74 " pdb=" SG CYS E 74 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CB CYS C 74 " pdb=" SG CYS C 74 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.50e+00 bond pdb=" N ASN A 262 " pdb=" CA ASN A 262 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.52e-02 4.33e+03 4.45e+00 bond pdb=" N ASN E 262 " pdb=" CA ASN E 262 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.52e-02 4.33e+03 4.40e+00 ... (remaining 25213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 33471 2.53 - 5.07: 640 5.07 - 7.60: 110 7.60 - 10.14: 3 10.14 - 12.67: 3 Bond angle restraints: 34227 Sorted by residual: angle pdb=" CA CYS C 54 " pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " ideal model delta sigma weight residual 114.40 127.07 -12.67 2.30e+00 1.89e-01 3.04e+01 angle pdb=" CA CYS E 54 " pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " ideal model delta sigma weight residual 114.40 127.04 -12.64 2.30e+00 1.89e-01 3.02e+01 angle pdb=" CA CYS A 54 " pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " ideal model delta sigma weight residual 114.40 127.03 -12.63 2.30e+00 1.89e-01 3.02e+01 angle pdb=" C CYS A 54 " pdb=" CA CYS A 54 " pdb=" CB CYS A 54 " ideal model delta sigma weight residual 109.51 101.96 7.55 1.71e+00 3.42e-01 1.95e+01 angle pdb=" C CYS E 54 " pdb=" CA CYS E 54 " pdb=" CB CYS E 54 " ideal model delta sigma weight residual 109.51 101.96 7.55 1.71e+00 3.42e-01 1.95e+01 ... (remaining 34222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 14677 21.26 - 42.53: 845 42.53 - 63.79: 261 63.79 - 85.06: 78 85.06 - 106.32: 36 Dihedral angle restraints: 15897 sinusoidal: 7236 harmonic: 8661 Sorted by residual: dihedral pdb=" CD ARG H 71 " pdb=" NE ARG H 71 " pdb=" CZ ARG H 71 " pdb=" NH1 ARG H 71 " ideal model delta sinusoidal sigma weight residual 0.00 85.81 -85.81 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CD ARG P 71 " pdb=" NE ARG P 71 " pdb=" CZ ARG P 71 " pdb=" NH1 ARG P 71 " ideal model delta sinusoidal sigma weight residual 0.00 85.81 -85.81 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CD ARG K 71 " pdb=" NE ARG K 71 " pdb=" CZ ARG K 71 " pdb=" NH1 ARG K 71 " ideal model delta sinusoidal sigma weight residual 0.00 85.81 -85.81 1 1.00e+01 1.00e-02 8.90e+01 ... (remaining 15894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3258 0.063 - 0.125: 578 0.125 - 0.188: 115 0.188 - 0.250: 15 0.250 - 0.313: 6 Chirality restraints: 3972 Sorted by residual: chirality pdb=" C1 MAN a 4 " pdb=" O3 BMA a 3 " pdb=" C2 MAN a 4 " pdb=" O5 MAN a 4 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.68e+02 chirality pdb=" C1 MAN S 4 " pdb=" O3 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.68e+02 chirality pdb=" C1 MAN W 4 " pdb=" O3 BMA W 3 " pdb=" C2 MAN W 4 " pdb=" O5 MAN W 4 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.67e+02 ... (remaining 3969 not shown) Planarity restraints: 4338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 1 " -0.307 2.00e-02 2.50e+03 2.65e-01 8.80e+02 pdb=" C7 NAG a 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG a 1 " -0.157 2.00e-02 2.50e+03 pdb=" N2 NAG a 1 " 0.470 2.00e-02 2.50e+03 pdb=" O7 NAG a 1 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " -0.307 2.00e-02 2.50e+03 2.65e-01 8.80e+02 pdb=" C7 NAG S 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " -0.157 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " 0.470 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " -0.307 2.00e-02 2.50e+03 2.65e-01 8.79e+02 pdb=" C7 NAG W 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " -0.157 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " 0.469 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " -0.081 2.00e-02 2.50e+03 ... (remaining 4335 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5062 2.79 - 3.32: 21161 3.32 - 3.85: 42632 3.85 - 4.37: 52283 4.37 - 4.90: 87566 Nonbonded interactions: 208704 Sorted by model distance: nonbonded pdb=" O GLY O 96 " pdb=" OH TYR Q 96 " model vdw 2.265 3.040 nonbonded pdb=" O GLY J 96 " pdb=" OH TYR M 96 " model vdw 2.265 3.040 nonbonded pdb=" O GLY G 96 " pdb=" OH TYR I 96 " model vdw 2.265 3.040 nonbonded pdb=" OG SER P 74 " pdb=" O ASP P 76C" model vdw 2.387 3.040 nonbonded pdb=" OG SER H 74 " pdb=" O ASP H 76C" model vdw 2.387 3.040 ... (remaining 208699 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'V' selection = chain 'Z' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.930 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: 0.040 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 25.060 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.005 0.070 25335 Z= 0.219 Angle : 0.939 28.827 34533 Z= 0.453 Chirality : 0.054 0.313 3972 Planarity : 0.026 0.444 4290 Dihedral : 15.937 106.323 10230 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.46 % Allowed : 12.64 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 2973 helix: -1.65 (0.23), residues: 414 sheet: -0.01 (0.16), residues: 915 loop : -1.05 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.118 0.012 ARG C 476 TYR 0.031 0.002 TYR R 49 PHE 0.024 0.002 PHE H 29 TRP 0.028 0.002 TRP E 479 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (25218) covalent geometry : angle 0.86045 / 0.44 (34227) SS BOND : bond 0.00562 / 0.31 ( 45) SS BOND : angle 1.50788 / 1.14 ( 90) hydrogen bonds : bond 0.20176 / 13.47 ( 663) hydrogen bonds : angle 8.10767 / 5.56 ( 1764) link_ALPHA1-3 : bond 0.04530 / 2.27 ( 3) link_ALPHA1-3 : angle 3.25723 / 2.22 ( 9) link_ALPHA1-6 : bond 0.03749 / 1.88 ( 3) link_ALPHA1-6 : angle 3.21217 / 2.12 ( 9) link_BETA1-4 : bond 0.03936 / 2.46 ( 18) link_BETA1-4 : angle 4.95144 / 3.51 ( 54) link_NAG-ASN : bond 0.00365 / 0.20 ( 48) link_NAG-ASN : angle 4.86448 / 3.18 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 459 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ILE cc_start: 0.8805 (mm) cc_final: 0.8529 (mm) REVERT: A 232 LYS cc_start: 0.8869 (mtmt) cc_final: 0.8305 (mmmt) REVERT: A 267 GLU cc_start: 0.6617 (mp0) cc_final: 0.6321 (mp0) REVERT: A 504 ARG cc_start: 0.7496 (mtm110) cc_final: 0.7288 (mtm110) REVERT: G 97 MET cc_start: 0.9027 (ptm) cc_final: 0.8720 (ptm) REVERT: G 100 GLN cc_start: 0.9045 (mt0) cc_final: 0.8752 (mt0) REVERT: I 42 LYS cc_start: 0.7520 (mttm) cc_final: 0.7305 (mtmt) REVERT: H 21 SER cc_start: 0.9040 (t) cc_final: 0.8692 (m) REVERT: H 72 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8249 (mt0) REVERT: H 76 TRP cc_start: 0.7491 (p-90) cc_final: 0.7048 (t60) REVERT: L 45 LYS cc_start: 0.8314 (ttpp) cc_final: 0.8003 (tttm) REVERT: L 53 LYS cc_start: 0.7925 (mttt) cc_final: 0.7682 (mtmm) REVERT: L 102 THR cc_start: 0.6971 (m) cc_final: 0.6644 (m) REVERT: C 95 MET cc_start: 0.9218 (ptm) cc_final: 0.8961 (ptm) REVERT: C 211 GLU cc_start: 0.8137 (tp30) cc_final: 0.7826 (tp30) REVERT: C 231 LYS cc_start: 0.8436 (mttm) cc_final: 0.8189 (mtmt) REVERT: C 232 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8344 (mmmt) REVERT: C 352 HIS cc_start: 0.8427 (m-70) cc_final: 0.8224 (m-70) REVERT: C 428 GLN cc_start: 0.7778 (mm110) cc_final: 0.7383 (mt0) REVERT: D 616 ASN cc_start: 0.8295 (p0) cc_final: 0.8046 (p0) REVERT: D 648 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8266 (tp30) REVERT: J 91 TYR cc_start: 0.8777 (m-80) cc_final: 0.8439 (m-80) REVERT: M 87 TYR cc_start: 0.8462 (m-80) cc_final: 0.8163 (m-80) REVERT: K 67 ILE cc_start: 0.8284 (mt) cc_final: 0.8057 (mt) REVERT: K 72 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8330 (mt0) REVERT: K 76 TRP cc_start: 0.7486 (p-90) cc_final: 0.7248 (p-90) REVERT: K 86 ASP cc_start: 0.7262 (m-30) cc_final: 0.6973 (m-30) REVERT: N 45 LYS cc_start: 0.8302 (ttpp) cc_final: 0.8018 (tttt) REVERT: E 95 MET cc_start: 0.9070 (ptm) cc_final: 0.8742 (ptm) REVERT: E 104 MET cc_start: 0.9289 (ttt) cc_final: 0.9013 (ttt) REVERT: E 232 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8284 (mmmt) REVERT: E 352 HIS cc_start: 0.8463 (m-70) cc_final: 0.8246 (m-70) REVERT: E 479 TRP cc_start: 0.7560 (m-10) cc_final: 0.6018 (m-10) REVERT: E 504 ARG cc_start: 0.7569 (mtm110) cc_final: 0.7288 (mtm110) REVERT: F 648 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8302 (tp30) REVERT: Q 87 TYR cc_start: 0.8411 (m-80) cc_final: 0.8109 (m-80) REVERT: P 21 SER cc_start: 0.8703 (t) cc_final: 0.8418 (m) REVERT: P 23 GLU cc_start: 0.8114 (tt0) cc_final: 0.7737 (mm-30) REVERT: P 28 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8258 (ttm-80) REVERT: P 86 ASP cc_start: 0.7283 (m-30) cc_final: 0.7064 (m-30) REVERT: R 53 LYS cc_start: 0.8001 (mttt) cc_final: 0.7627 (mtmm) outliers start: 12 outliers final: 1 residues processed: 467 average time/residue: 0.6611 time to fit residues: 351.3112 Evaluate side-chains 394 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 391 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain P residue 72 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 195 ASN A 246 GLN A 377 ASN B 653 GLN I 79 GLN I 95 GLN H 52 ASN L 27 HIS L 52 ASN C 130 GLN C 136 ASN C 195 ASN D 630 GLN D 653 GLN M 69 ASN M 79 GLN M 95 GLN K 52 ASN N 27 HIS E 195 ASN E 377 ASN F 630 GLN F 653 GLN Q 79 GLN Q 95 GLN P 52 ASN R 27 HIS R 52 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.166201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.132328 restraints weight = 23696.912| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.60 r_work: 0.3035 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25335 Z= 0.144 Angle : 0.616 7.178 34533 Z= 0.309 Chirality : 0.046 0.217 3972 Planarity : 0.005 0.077 4290 Dihedral : 8.805 76.284 4767 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.95 % Allowed : 14.10 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 2973 helix: -0.37 (0.26), residues: 432 sheet: 0.29 (0.16), residues: 897 loop : -0.62 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 429 TYR 0.020 0.001 TYR N 49 PHE 0.019 0.002 PHE A 391 TRP 0.020 0.002 TRP E 479 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (25218) covalent geometry : angle 0.58787 / 0.30 (34227) SS BOND : bond 0.00416 / 0.28 ( 45) SS BOND : angle 1.13584 / 0.85 ( 90) hydrogen bonds : bond 0.04265 / 2.89 ( 663) hydrogen bonds : angle 5.67263 / 3.84 ( 1764) link_ALPHA1-3 : bond 0.01686 / 0.85 ( 3) link_ALPHA1-3 : angle 1.51681 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00749 / 0.38 ( 3) link_ALPHA1-6 : angle 1.90410 / 1.33 ( 9) link_BETA1-4 : bond 0.00483 / 0.29 ( 18) link_BETA1-4 : angle 2.52435 / 1.82 ( 54) link_NAG-ASN : bond 0.00241 / 0.15 ( 48) link_NAG-ASN : angle 2.27180 / 1.47 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 423 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 215 ILE cc_start: 0.9102 (mm) cc_final: 0.8866 (mm) REVERT: A 231 LYS cc_start: 0.8418 (mttt) cc_final: 0.8192 (mttm) REVERT: A 232 LYS cc_start: 0.8925 (mtmt) cc_final: 0.8111 (mmmt) REVERT: A 267 GLU cc_start: 0.6679 (mp0) cc_final: 0.6360 (mp0) REVERT: A 347 LYS cc_start: 0.9001 (tttp) cc_final: 0.8257 (pttm) REVERT: B 575 GLN cc_start: 0.7277 (tt0) cc_final: 0.6951 (tp-100) REVERT: B 634 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8508 (mt-10) REVERT: G 18 LEU cc_start: 0.7888 (tp) cc_final: 0.7670 (tp) REVERT: G 91 TYR cc_start: 0.8409 (m-80) cc_final: 0.8172 (m-80) REVERT: G 97 MET cc_start: 0.9058 (ptm) cc_final: 0.8773 (ptm) REVERT: G 100 GLN cc_start: 0.9132 (mt0) cc_final: 0.8811 (mt0) REVERT: I 42 LYS cc_start: 0.7418 (mttm) cc_final: 0.7070 (mtmm) REVERT: I 50 ASP cc_start: 0.8188 (m-30) cc_final: 0.7933 (m-30) REVERT: H 72 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: H 76 TRP cc_start: 0.7305 (p-90) cc_final: 0.6990 (t60) REVERT: H 100 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7157 (mmtm) REVERT: L 53 LYS cc_start: 0.7840 (mttt) cc_final: 0.7259 (mtmm) REVERT: C 87 GLU cc_start: 0.8682 (tp30) cc_final: 0.8446 (tp30) REVERT: C 211 GLU cc_start: 0.8044 (tp30) cc_final: 0.7583 (tp30) REVERT: C 232 LYS cc_start: 0.8937 (mtmt) cc_final: 0.8074 (mmtt) REVERT: C 340 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: C 347 LYS cc_start: 0.9002 (tttp) cc_final: 0.8466 (tppt) REVERT: C 419 ARG cc_start: 0.8585 (mtp180) cc_final: 0.8294 (mtm180) REVERT: C 428 GLN cc_start: 0.7949 (mm110) cc_final: 0.7389 (mt0) REVERT: D 530 MET cc_start: 0.9203 (mtp) cc_final: 0.9001 (mtm) REVERT: D 575 GLN cc_start: 0.7409 (tt0) cc_final: 0.7049 (tp40) REVERT: J 91 TYR cc_start: 0.8665 (m-80) cc_final: 0.8337 (m-80) REVERT: K 54 TYR cc_start: 0.8896 (m-80) cc_final: 0.8598 (m-80) REVERT: K 67 ILE cc_start: 0.8294 (mt) cc_final: 0.8087 (mt) REVERT: K 72 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: K 76 TRP cc_start: 0.7514 (p-90) cc_final: 0.7180 (t60) REVERT: N 45 LYS cc_start: 0.8407 (ttpp) cc_final: 0.7842 (tttt) REVERT: E 104 MET cc_start: 0.9262 (ttt) cc_final: 0.8929 (ttt) REVERT: E 232 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8081 (mmmt) REVERT: E 419 ARG cc_start: 0.8674 (mtm180) cc_final: 0.8392 (mtm180) REVERT: E 479 TRP cc_start: 0.7718 (m-10) cc_final: 0.6070 (m-10) REVERT: E 504 ARG cc_start: 0.7581 (mtm110) cc_final: 0.7247 (mtt90) REVERT: F 575 GLN cc_start: 0.7427 (tt0) cc_final: 0.7160 (tp40) REVERT: F 648 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8110 (tp30) REVERT: P 76 TRP cc_start: 0.7354 (p-90) cc_final: 0.6911 (t60) REVERT: R 45 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7610 (pptt) REVERT: R 53 LYS cc_start: 0.7873 (mttt) cc_final: 0.7329 (mtmm) outliers start: 51 outliers final: 16 residues processed: 450 average time/residue: 0.6707 time to fit residues: 343.7176 Evaluate side-chains 426 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 406 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 100 LYS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain P residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 79 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 377 ASN B 616 ASN G 81 GLN I 95 GLN C 136 ASN C 432 GLN D 616 ASN J 3 GLN M 95 GLN K 39 GLN K 52 ASN N 52 ASN E 377 ASN Q 69 ASN Q 95 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.156974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.128272 restraints weight = 23596.237| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.53 r_work: 0.2975 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25335 Z= 0.230 Angle : 0.679 8.128 34533 Z= 0.344 Chirality : 0.049 0.288 3972 Planarity : 0.005 0.046 4290 Dihedral : 7.928 62.600 4767 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.22 % Allowed : 13.56 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 2973 helix: 0.01 (0.26), residues: 414 sheet: 0.26 (0.16), residues: 915 loop : -0.61 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 71 TYR 0.022 0.002 TYR R 49 PHE 0.025 0.002 PHE A 391 TRP 0.018 0.003 TRP E 479 HIS 0.007 0.001 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (25218) covalent geometry : angle 0.65259 / 0.34 (34227) SS BOND : bond 0.00489 / 0.31 ( 45) SS BOND : angle 1.40497 / 1.02 ( 90) hydrogen bonds : bond 0.04993 / 3.32 ( 663) hydrogen bonds : angle 5.50467 / 3.73 ( 1764) link_ALPHA1-3 : bond 0.01668 / 0.84 ( 3) link_ALPHA1-3 : angle 0.96080 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00426 / 0.21 ( 3) link_ALPHA1-6 : angle 2.39806 / 1.70 ( 9) link_BETA1-4 : bond 0.00370 / 0.23 ( 18) link_BETA1-4 : angle 2.30636 / 1.68 ( 54) link_NAG-ASN : bond 0.00441 / 0.27 ( 48) link_NAG-ASN : angle 2.40897 / 1.60 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 410 time to evaluate : 0.856 Fit side-chains REVERT: A 114 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: A 232 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8087 (mmmt) REVERT: A 267 GLU cc_start: 0.6852 (mp0) cc_final: 0.6551 (mp0) REVERT: A 347 LYS cc_start: 0.9045 (tttp) cc_final: 0.8434 (tppt) REVERT: A 479 TRP cc_start: 0.7896 (m-10) cc_final: 0.7402 (m-10) REVERT: B 575 GLN cc_start: 0.7379 (tt0) cc_final: 0.7090 (tp-100) REVERT: G 97 MET cc_start: 0.9179 (ptm) cc_final: 0.8864 (ptm) REVERT: G 100 GLN cc_start: 0.9056 (mt0) cc_final: 0.8716 (mt0) REVERT: I 50 ASP cc_start: 0.8493 (m-30) cc_final: 0.8237 (m-30) REVERT: H 72 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: H 76 TRP cc_start: 0.7462 (p-90) cc_final: 0.7113 (t60) REVERT: H 100 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.6363 (m-80) REVERT: H 100 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7572 (mmtm) REVERT: L 53 LYS cc_start: 0.8199 (mttt) cc_final: 0.7576 (mtmm) REVERT: C 211 GLU cc_start: 0.8233 (tp30) cc_final: 0.7801 (tp30) REVERT: C 267 GLU cc_start: 0.6810 (mp0) cc_final: 0.6539 (mp0) REVERT: C 340 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: C 347 LYS cc_start: 0.9015 (tttp) cc_final: 0.8543 (tppt) REVERT: C 419 ARG cc_start: 0.8657 (mtp180) cc_final: 0.8442 (mtm180) REVERT: C 426 MET cc_start: 0.8417 (tpt) cc_final: 0.7967 (tpp) REVERT: C 428 GLN cc_start: 0.8154 (mm110) cc_final: 0.7542 (mt0) REVERT: D 530 MET cc_start: 0.9277 (mtp) cc_final: 0.9050 (mtm) REVERT: D 575 GLN cc_start: 0.7574 (tt0) cc_final: 0.7152 (tp-100) REVERT: K 23 GLU cc_start: 0.8297 (tt0) cc_final: 0.7646 (tp30) REVERT: K 54 TYR cc_start: 0.9045 (m-80) cc_final: 0.8737 (m-80) REVERT: K 76 TRP cc_start: 0.7624 (p-90) cc_final: 0.7391 (p-90) REVERT: K 86 ASP cc_start: 0.7146 (m-30) cc_final: 0.6897 (m-30) REVERT: K 100 ASP cc_start: 0.8449 (m-30) cc_final: 0.8046 (m-30) REVERT: N 45 LYS cc_start: 0.8350 (ttpp) cc_final: 0.7875 (tttt) REVERT: E 104 MET cc_start: 0.9309 (ttt) cc_final: 0.9002 (ttt) REVERT: E 114 GLN cc_start: 0.8530 (tt0) cc_final: 0.8286 (tt0) REVERT: E 232 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8153 (mmmt) REVERT: E 424 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8431 (mp) REVERT: E 426 MET cc_start: 0.8474 (tpt) cc_final: 0.8223 (tpp) REVERT: E 428 GLN cc_start: 0.8110 (mm110) cc_final: 0.7359 (mm-40) REVERT: E 504 ARG cc_start: 0.7601 (mtm110) cc_final: 0.7336 (mtt90) REVERT: F 530 MET cc_start: 0.9302 (mtp) cc_final: 0.9079 (mtp) REVERT: F 575 GLN cc_start: 0.7521 (tt0) cc_final: 0.7288 (tp40) REVERT: F 648 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8278 (tp30) REVERT: O 23 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.6572 (mpt90) REVERT: P 76 TRP cc_start: 0.7690 (p-90) cc_final: 0.6969 (t60) REVERT: P 100 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.6821 (m-10) REVERT: P 100 LYS cc_start: 0.7931 (tmmt) cc_final: 0.7700 (mmtm) REVERT: R 53 LYS cc_start: 0.8266 (mttt) cc_final: 0.7668 (mtmm) outliers start: 84 outliers final: 46 residues processed: 460 average time/residue: 0.6503 time to fit residues: 342.2342 Evaluate side-chains 448 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 394 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 LYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 100 TYR Chi-restraints excluded: chain P residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 262 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 234 optimal weight: 0.1980 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 278 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN I 95 GLN C 432 GLN D 616 ASN D 652 GLN M 95 GLN K 52 ASN E 136 ASN E 377 ASN E 432 GLN Q 69 ASN Q 95 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.158706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.131630 restraints weight = 23530.805| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.33 r_work: 0.3052 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25335 Z= 0.146 Angle : 0.574 6.454 34533 Z= 0.290 Chirality : 0.045 0.257 3972 Planarity : 0.004 0.035 4290 Dihedral : 7.151 59.705 4764 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.72 % Allowed : 14.83 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 2973 helix: 0.32 (0.26), residues: 432 sheet: 0.23 (0.16), residues: 963 loop : -0.39 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 19 TYR 0.018 0.001 TYR N 49 PHE 0.018 0.002 PHE A 391 TRP 0.017 0.002 TRP P 50 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (25218) covalent geometry : angle 0.55015 / 0.29 (34227) SS BOND : bond 0.00344 / 0.23 ( 45) SS BOND : angle 1.01551 / 0.73 ( 90) hydrogen bonds : bond 0.04031 / 2.70 ( 663) hydrogen bonds : angle 5.23445 / 3.53 ( 1764) link_ALPHA1-3 : bond 0.01477 / 0.74 ( 3) link_ALPHA1-3 : angle 1.01940 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00172 / 0.09 ( 3) link_ALPHA1-6 : angle 2.38400 / 1.70 ( 9) link_BETA1-4 : bond 0.00464 / 0.28 ( 18) link_BETA1-4 : angle 2.00496 / 1.48 ( 54) link_NAG-ASN : bond 0.00250 / 0.15 ( 48) link_NAG-ASN : angle 2.13995 / 1.44 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 399 time to evaluate : 0.962 Fit side-chains REVERT: A 114 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: A 231 LYS cc_start: 0.8524 (mttm) cc_final: 0.8291 (mttt) REVERT: A 232 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8208 (mmmt) REVERT: A 267 GLU cc_start: 0.6870 (mp0) cc_final: 0.6620 (mp0) REVERT: A 347 LYS cc_start: 0.8993 (tttp) cc_final: 0.8491 (tppt) REVERT: A 428 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7469 (mt0) REVERT: A 479 TRP cc_start: 0.7690 (m-10) cc_final: 0.7249 (m-10) REVERT: G 97 MET cc_start: 0.9031 (ptm) cc_final: 0.8780 (ptm) REVERT: G 100 GLN cc_start: 0.8839 (mt0) cc_final: 0.8496 (mt0) REVERT: I 50 ASP cc_start: 0.8407 (m-30) cc_final: 0.8129 (m-30) REVERT: H 72 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: H 76 TRP cc_start: 0.7483 (p-90) cc_final: 0.7232 (t60) REVERT: H 100 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: L 53 LYS cc_start: 0.8130 (mttt) cc_final: 0.7724 (mtmm) REVERT: C 211 GLU cc_start: 0.8256 (tp30) cc_final: 0.7866 (tp30) REVERT: C 232 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8258 (mmmt) REVERT: C 267 GLU cc_start: 0.6750 (mp0) cc_final: 0.6550 (mp0) REVERT: C 340 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: C 347 LYS cc_start: 0.8960 (tttp) cc_final: 0.8589 (tppt) REVERT: C 426 MET cc_start: 0.8194 (tpt) cc_final: 0.7979 (tpp) REVERT: C 428 GLN cc_start: 0.7903 (mm110) cc_final: 0.7431 (mm-40) REVERT: C 479 TRP cc_start: 0.7708 (m-10) cc_final: 0.6584 (m-10) REVERT: K 23 GLU cc_start: 0.8079 (tt0) cc_final: 0.7637 (tp30) REVERT: K 54 TYR cc_start: 0.8944 (m-80) cc_final: 0.8664 (m-80) REVERT: K 76 TRP cc_start: 0.7682 (p-90) cc_final: 0.7413 (p-90) REVERT: K 100 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: K 100 ASP cc_start: 0.8396 (m-30) cc_final: 0.8097 (m-30) REVERT: N 45 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7763 (tttt) REVERT: E 104 MET cc_start: 0.9219 (ttt) cc_final: 0.8880 (ttt) REVERT: E 114 GLN cc_start: 0.8357 (tt0) cc_final: 0.8123 (tt0) REVERT: E 232 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8257 (mmmt) REVERT: E 347 LYS cc_start: 0.8921 (tttp) cc_final: 0.8489 (tppt) REVERT: E 424 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8407 (mp) REVERT: E 428 GLN cc_start: 0.7939 (mm110) cc_final: 0.7348 (mm-40) REVERT: E 504 ARG cc_start: 0.7189 (mtm110) cc_final: 0.6928 (mtt90) REVERT: F 530 MET cc_start: 0.9165 (mtp) cc_final: 0.8908 (mtp) REVERT: O 23 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6661 (mpt90) REVERT: Q 85 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: P 76 TRP cc_start: 0.7736 (p-90) cc_final: 0.7119 (t60) REVERT: R 53 LYS cc_start: 0.8155 (mttt) cc_final: 0.7772 (mtmm) outliers start: 71 outliers final: 35 residues processed: 436 average time/residue: 0.6560 time to fit residues: 328.3094 Evaluate side-chains 435 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 391 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 100 TYR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain R residue 51 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 118 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 295 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 432 GLN B 630 GLN I 95 GLN C 432 GLN D 616 ASN M 95 GLN E 136 ASN E 377 ASN Q 69 ASN Q 95 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.158539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.130119 restraints weight = 23551.113| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.47 r_work: 0.3022 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25335 Z= 0.155 Angle : 0.570 6.345 34533 Z= 0.288 Chirality : 0.045 0.261 3972 Planarity : 0.004 0.034 4290 Dihedral : 6.797 59.854 4764 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.14 % Allowed : 14.75 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 2973 helix: 0.51 (0.26), residues: 432 sheet: 0.24 (0.16), residues: 963 loop : -0.30 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 71 TYR 0.018 0.001 TYR R 49 PHE 0.016 0.002 PHE A 391 TRP 0.016 0.002 TRP K 50 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (25218) covalent geometry : angle 0.54675 / 0.28 (34227) SS BOND : bond 0.00346 / 0.23 ( 45) SS BOND : angle 0.98722 / 0.69 ( 90) hydrogen bonds : bond 0.04057 / 2.71 ( 663) hydrogen bonds : angle 5.15513 / 3.48 ( 1764) link_ALPHA1-3 : bond 0.01460 / 0.73 ( 3) link_ALPHA1-3 : angle 0.95086 / 0.71 ( 9) link_ALPHA1-6 : bond 0.00063 / 0.03 ( 3) link_ALPHA1-6 : angle 2.35932 / 1.67 ( 9) link_BETA1-4 : bond 0.00459 / 0.27 ( 18) link_BETA1-4 : angle 1.93846 / 1.41 ( 54) link_NAG-ASN : bond 0.00279 / 0.17 ( 48) link_NAG-ASN : angle 2.11509 / 1.43 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 396 time to evaluate : 0.784 Fit side-chains REVERT: A 232 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8068 (mmmt) REVERT: A 267 GLU cc_start: 0.6895 (mp0) cc_final: 0.6597 (mp0) REVERT: A 347 LYS cc_start: 0.9020 (tttp) cc_final: 0.8426 (tppt) REVERT: A 428 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7325 (mt0) REVERT: A 479 TRP cc_start: 0.7777 (m-10) cc_final: 0.7348 (m-10) REVERT: G 97 MET cc_start: 0.9112 (ptm) cc_final: 0.8812 (ptm) REVERT: G 100 GLN cc_start: 0.9008 (mt0) cc_final: 0.8671 (mt0) REVERT: I 50 ASP cc_start: 0.8397 (m-30) cc_final: 0.8131 (m-30) REVERT: H 56 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7634 (mp10) REVERT: H 72 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: H 76 TRP cc_start: 0.7411 (p-90) cc_final: 0.7060 (t60) REVERT: H 100 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6283 (m-80) REVERT: L 45 LYS cc_start: 0.8298 (ttpp) cc_final: 0.8067 (ttpp) REVERT: L 53 LYS cc_start: 0.8034 (mttt) cc_final: 0.7364 (mtmm) REVERT: C 211 GLU cc_start: 0.8235 (tp30) cc_final: 0.7783 (tp30) REVERT: C 232 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8217 (mmpt) REVERT: C 267 GLU cc_start: 0.6848 (mp0) cc_final: 0.6587 (mp0) REVERT: C 340 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: C 347 LYS cc_start: 0.8978 (tttp) cc_final: 0.8525 (tppt) REVERT: C 426 MET cc_start: 0.8380 (tpt) cc_final: 0.7913 (tpp) REVERT: C 428 GLN cc_start: 0.8034 (mm110) cc_final: 0.7393 (mm-40) REVERT: K 23 GLU cc_start: 0.8183 (tt0) cc_final: 0.7543 (tp30) REVERT: K 54 TYR cc_start: 0.9053 (m-80) cc_final: 0.8787 (m-80) REVERT: K 100 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: K 100 ASP cc_start: 0.8384 (m-30) cc_final: 0.8009 (m-30) REVERT: N 45 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7752 (tttt) REVERT: E 104 MET cc_start: 0.9352 (ttt) cc_final: 0.9030 (ttt) REVERT: E 114 GLN cc_start: 0.8405 (tt0) cc_final: 0.8196 (tt0) REVERT: E 215 ILE cc_start: 0.8948 (mm) cc_final: 0.8741 (mp) REVERT: E 232 LYS cc_start: 0.8925 (mtmt) cc_final: 0.8117 (mmmt) REVERT: E 347 LYS cc_start: 0.8979 (tttp) cc_final: 0.8421 (tppt) REVERT: E 424 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8367 (mp) REVERT: E 428 GLN cc_start: 0.7932 (mm110) cc_final: 0.7212 (mm-40) REVERT: E 504 ARG cc_start: 0.7561 (mtm110) cc_final: 0.7282 (mtt90) REVERT: F 530 MET cc_start: 0.9254 (mtp) cc_final: 0.8988 (mtp) REVERT: O 23 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6649 (mpt90) REVERT: Q 85 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: P 76 TRP cc_start: 0.7680 (p-90) cc_final: 0.6978 (t60) REVERT: P 100 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.6734 (m-10) REVERT: R 53 LYS cc_start: 0.8097 (mttt) cc_final: 0.7498 (mtmm) outliers start: 82 outliers final: 48 residues processed: 450 average time/residue: 0.6462 time to fit residues: 332.6005 Evaluate side-chains 450 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 392 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 100 TYR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain P residue 100 TYR Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain R residue 51 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 289 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 432 GLN B 616 ASN I 95 GLN C 136 ASN C 377 ASN C 432 GLN D 616 ASN M 95 GLN E 136 ASN E 246 GLN E 377 ASN Q 69 ASN Q 95 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.157023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.128005 restraints weight = 23595.092| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.50 r_work: 0.2994 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25335 Z= 0.206 Angle : 0.618 6.888 34533 Z= 0.313 Chirality : 0.047 0.279 3972 Planarity : 0.005 0.035 4290 Dihedral : 6.807 58.085 4761 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.83 % Allowed : 14.64 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 2973 helix: 0.43 (0.26), residues: 432 sheet: 0.17 (0.16), residues: 963 loop : -0.33 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 429 TYR 0.021 0.002 TYR N 49 PHE 0.018 0.002 PHE A 391 TRP 0.017 0.002 TRP H 50 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (25218) covalent geometry : angle 0.59365 / 0.31 (34227) SS BOND : bond 0.00424 / 0.28 ( 45) SS BOND : angle 1.15005 / 0.79 ( 90) hydrogen bonds : bond 0.04504 / 2.99 ( 663) hydrogen bonds : angle 5.24994 / 3.54 ( 1764) link_ALPHA1-3 : bond 0.01405 / 0.70 ( 3) link_ALPHA1-3 : angle 1.03381 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00076 / 0.04 ( 3) link_ALPHA1-6 : angle 2.34033 / 1.65 ( 9) link_BETA1-4 : bond 0.00493 / 0.30 ( 18) link_BETA1-4 : angle 2.03539 / 1.48 ( 54) link_NAG-ASN : bond 0.00388 / 0.24 ( 48) link_NAG-ASN : angle 2.26123 / 1.52 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 392 time to evaluate : 0.924 Fit side-chains REVERT: A 114 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: A 232 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8076 (mmmt) REVERT: A 267 GLU cc_start: 0.6873 (mp0) cc_final: 0.6665 (mp0) REVERT: A 347 LYS cc_start: 0.8993 (tttp) cc_final: 0.8408 (tppt) REVERT: A 428 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7384 (mt0) REVERT: A 479 TRP cc_start: 0.7818 (m-10) cc_final: 0.7333 (m-10) REVERT: B 575 GLN cc_start: 0.7387 (tt0) cc_final: 0.7171 (tp-100) REVERT: B 601 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8618 (mtpm) REVERT: G 97 MET cc_start: 0.9159 (ptm) cc_final: 0.8861 (ptm) REVERT: G 100 GLN cc_start: 0.9041 (mt0) cc_final: 0.8725 (mt0) REVERT: I 50 ASP cc_start: 0.8464 (m-30) cc_final: 0.8192 (m-30) REVERT: H 56 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: H 72 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: H 76 TRP cc_start: 0.7440 (p-90) cc_final: 0.7070 (t60) REVERT: H 100 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: L 45 LYS cc_start: 0.8328 (ttpp) cc_final: 0.8052 (ttpp) REVERT: L 53 LYS cc_start: 0.8089 (mttt) cc_final: 0.7397 (mtmm) REVERT: C 114 GLN cc_start: 0.7952 (tt0) cc_final: 0.7549 (tt0) REVERT: C 211 GLU cc_start: 0.8276 (tp30) cc_final: 0.7802 (tp30) REVERT: C 232 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8239 (mmpt) REVERT: C 267 GLU cc_start: 0.6866 (mp0) cc_final: 0.6618 (mp0) REVERT: C 340 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: C 347 LYS cc_start: 0.8964 (tttp) cc_final: 0.8524 (tppt) REVERT: C 426 MET cc_start: 0.8387 (tpt) cc_final: 0.7956 (tpp) REVERT: C 428 GLN cc_start: 0.8050 (mm110) cc_final: 0.7395 (mm-40) REVERT: D 575 GLN cc_start: 0.7249 (tt0) cc_final: 0.6996 (tp-100) REVERT: K 23 GLU cc_start: 0.8319 (tt0) cc_final: 0.7646 (tp30) REVERT: K 54 TYR cc_start: 0.9047 (m-80) cc_final: 0.8752 (m-80) REVERT: K 100 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.6500 (m-80) REVERT: K 100 ASP cc_start: 0.8442 (m-30) cc_final: 0.8071 (m-30) REVERT: N 45 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7718 (tttt) REVERT: E 104 MET cc_start: 0.9365 (ttt) cc_final: 0.9043 (ttt) REVERT: E 114 GLN cc_start: 0.8368 (tt0) cc_final: 0.8166 (tt0) REVERT: E 129 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8728 (mt) REVERT: E 232 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8141 (mmmt) REVERT: E 347 LYS cc_start: 0.8979 (tttp) cc_final: 0.8437 (tppt) REVERT: E 424 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8409 (mp) REVERT: E 428 GLN cc_start: 0.8016 (mm110) cc_final: 0.7434 (mm-40) REVERT: E 504 ARG cc_start: 0.7589 (mtm110) cc_final: 0.7309 (mtt90) REVERT: F 530 MET cc_start: 0.9273 (mtp) cc_final: 0.8973 (mtp) REVERT: O 23 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6661 (mpt90) REVERT: Q 85 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: P 76 TRP cc_start: 0.7681 (p-90) cc_final: 0.6870 (t60) REVERT: P 100 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6792 (m-10) REVERT: R 53 LYS cc_start: 0.8120 (mttt) cc_final: 0.7501 (mtmm) outliers start: 100 outliers final: 57 residues processed: 458 average time/residue: 0.6315 time to fit residues: 331.7747 Evaluate side-chains 457 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 387 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 TYR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain P residue 100 TYR Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 134 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 432 GLN B 616 ASN I 95 GLN C 432 GLN D 616 ASN M 95 GLN E 136 ASN E 377 ASN Q 69 ASN Q 95 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.158534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.128346 restraints weight = 23592.845| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.64 r_work: 0.3021 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25335 Z= 0.146 Angle : 0.560 7.531 34533 Z= 0.284 Chirality : 0.045 0.268 3972 Planarity : 0.004 0.034 4290 Dihedral : 6.455 59.839 4761 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.10 % Allowed : 15.56 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 2973 helix: 0.69 (0.26), residues: 432 sheet: 0.17 (0.16), residues: 927 loop : -0.24 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 178 TYR 0.018 0.001 TYR R 49 PHE 0.015 0.002 PHE A 391 TRP 0.017 0.002 TRP P 50 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (25218) covalent geometry : angle 0.53674 / 0.28 (34227) SS BOND : bond 0.00340 / 0.23 ( 45) SS BOND : angle 0.92193 / 0.63 ( 90) hydrogen bonds : bond 0.03934 / 2.63 ( 663) hydrogen bonds : angle 5.10614 / 3.44 ( 1764) link_ALPHA1-3 : bond 0.01407 / 0.71 ( 3) link_ALPHA1-3 : angle 0.98723 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00146 / 0.07 ( 3) link_ALPHA1-6 : angle 2.33158 / 1.62 ( 9) link_BETA1-4 : bond 0.00465 / 0.28 ( 18) link_BETA1-4 : angle 1.87101 / 1.36 ( 54) link_NAG-ASN : bond 0.00251 / 0.15 ( 48) link_NAG-ASN : angle 2.10531 / 1.43 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 396 time to evaluate : 0.809 Fit side-chains REVERT: A 114 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: A 347 LYS cc_start: 0.8996 (tttp) cc_final: 0.8414 (tppt) REVERT: A 357 THR cc_start: 0.8665 (t) cc_final: 0.8445 (m) REVERT: A 428 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7314 (mt0) REVERT: A 479 TRP cc_start: 0.7725 (m-10) cc_final: 0.7285 (m-10) REVERT: G 97 MET cc_start: 0.9110 (ptm) cc_final: 0.8791 (ptm) REVERT: G 100 GLN cc_start: 0.9015 (mt0) cc_final: 0.8682 (mt0) REVERT: I 50 ASP cc_start: 0.8425 (m-30) cc_final: 0.8161 (m-30) REVERT: H 56 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: H 76 TRP cc_start: 0.7462 (p-90) cc_final: 0.7085 (t60) REVERT: H 100 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.6220 (m-80) REVERT: L 45 LYS cc_start: 0.8232 (ttpp) cc_final: 0.8001 (ttpp) REVERT: L 53 LYS cc_start: 0.8020 (mttt) cc_final: 0.7338 (mtmm) REVERT: C 114 GLN cc_start: 0.7893 (tt0) cc_final: 0.7481 (tt0) REVERT: C 211 GLU cc_start: 0.8238 (tp30) cc_final: 0.7776 (tp30) REVERT: C 232 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8109 (mmmt) REVERT: C 267 GLU cc_start: 0.6858 (mp0) cc_final: 0.6605 (mp0) REVERT: C 340 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: C 347 LYS cc_start: 0.8969 (tttp) cc_final: 0.8525 (tppt) REVERT: C 426 MET cc_start: 0.8333 (tpt) cc_final: 0.8041 (tpp) REVERT: C 428 GLN cc_start: 0.7975 (mm110) cc_final: 0.7283 (mm-40) REVERT: K 23 GLU cc_start: 0.8278 (tt0) cc_final: 0.7607 (tp30) REVERT: K 54 TYR cc_start: 0.9063 (m-80) cc_final: 0.8784 (m-80) REVERT: K 100 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: K 100 ASP cc_start: 0.8404 (m-30) cc_final: 0.8031 (m-30) REVERT: N 45 LYS cc_start: 0.8139 (ttpp) cc_final: 0.7654 (tttt) REVERT: E 104 MET cc_start: 0.9355 (ttt) cc_final: 0.9005 (ttt) REVERT: E 129 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8691 (mt) REVERT: E 232 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8188 (mmmt) REVERT: E 347 LYS cc_start: 0.8973 (tttp) cc_final: 0.8427 (tppt) REVERT: E 424 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8375 (mp) REVERT: E 428 GLN cc_start: 0.7910 (mm110) cc_final: 0.7177 (mm-40) REVERT: E 504 ARG cc_start: 0.7560 (mtm110) cc_final: 0.7273 (mtt90) REVERT: F 530 MET cc_start: 0.9261 (mtp) cc_final: 0.8977 (mtp) REVERT: O 23 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6673 (mpt90) REVERT: Q 85 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7184 (m-30) REVERT: P 76 TRP cc_start: 0.7624 (p-90) cc_final: 0.6877 (t60) REVERT: R 53 LYS cc_start: 0.8091 (mttt) cc_final: 0.7485 (mtmm) outliers start: 81 outliers final: 51 residues processed: 452 average time/residue: 0.6317 time to fit residues: 326.6236 Evaluate side-chains 450 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 389 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 TYR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 178 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 290 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 89 optimal weight: 0.0000 chunk 81 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 432 GLN B 616 ASN I 95 GLN C 432 GLN D 616 ASN M 95 GLN K 56 GLN E 136 ASN E 377 ASN Q 69 ASN Q 95 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.158151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132427 restraints weight = 23528.776| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.39 r_work: 0.3014 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25335 Z= 0.163 Angle : 0.576 9.406 34533 Z= 0.291 Chirality : 0.046 0.271 3972 Planarity : 0.004 0.038 4290 Dihedral : 6.351 58.264 4758 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.33 % Allowed : 15.40 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 2973 helix: 0.69 (0.26), residues: 432 sheet: 0.17 (0.16), residues: 927 loop : -0.25 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 178 TYR 0.020 0.001 TYR N 49 PHE 0.016 0.002 PHE A 391 TRP 0.016 0.002 TRP K 50 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (25218) covalent geometry : angle 0.55324 / 0.29 (34227) SS BOND : bond 0.00359 / 0.24 ( 45) SS BOND : angle 0.96423 / 0.66 ( 90) hydrogen bonds : bond 0.04070 / 2.71 ( 663) hydrogen bonds : angle 5.11682 / 3.45 ( 1764) link_ALPHA1-3 : bond 0.01379 / 0.69 ( 3) link_ALPHA1-3 : angle 1.02724 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00145 / 0.07 ( 3) link_ALPHA1-6 : angle 2.26182 / 1.56 ( 9) link_BETA1-4 : bond 0.00482 / 0.29 ( 18) link_BETA1-4 : angle 1.89829 / 1.38 ( 54) link_NAG-ASN : bond 0.00290 / 0.18 ( 48) link_NAG-ASN : angle 2.13196 / 1.45 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 395 time to evaluate : 0.707 Fit side-chains REVERT: A 114 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: A 232 LYS cc_start: 0.8981 (mtmp) cc_final: 0.8000 (mmmt) REVERT: A 347 LYS cc_start: 0.9002 (tttp) cc_final: 0.8435 (tppt) REVERT: A 428 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7367 (mt0) REVERT: A 479 TRP cc_start: 0.7742 (m-10) cc_final: 0.7343 (m-10) REVERT: G 97 MET cc_start: 0.9120 (ptm) cc_final: 0.8796 (ptm) REVERT: G 100 GLN cc_start: 0.9030 (mt0) cc_final: 0.8702 (mt0) REVERT: I 50 ASP cc_start: 0.8457 (m-30) cc_final: 0.8191 (m-30) REVERT: H 56 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: H 76 TRP cc_start: 0.7484 (p-90) cc_final: 0.7088 (t60) REVERT: H 100 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: L 45 LYS cc_start: 0.8301 (ttpp) cc_final: 0.8035 (ttpp) REVERT: L 53 LYS cc_start: 0.8033 (mttt) cc_final: 0.7365 (mtmm) REVERT: C 114 GLN cc_start: 0.7797 (tt0) cc_final: 0.7401 (tt0) REVERT: C 211 GLU cc_start: 0.8256 (tp30) cc_final: 0.7790 (tp30) REVERT: C 232 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8108 (mmmt) REVERT: C 267 GLU cc_start: 0.6870 (mp0) cc_final: 0.6616 (mp0) REVERT: C 340 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: C 347 LYS cc_start: 0.8977 (tttp) cc_final: 0.8534 (tppt) REVERT: C 426 MET cc_start: 0.8367 (tpt) cc_final: 0.8056 (tpp) REVERT: C 428 GLN cc_start: 0.7997 (mm110) cc_final: 0.7311 (mm-40) REVERT: K 23 GLU cc_start: 0.8324 (tt0) cc_final: 0.7615 (tp30) REVERT: K 54 TYR cc_start: 0.9063 (m-80) cc_final: 0.8785 (m-80) REVERT: K 100 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: K 100 ASP cc_start: 0.8413 (m-30) cc_final: 0.8038 (m-30) REVERT: N 45 LYS cc_start: 0.8116 (ttpp) cc_final: 0.7653 (tttt) REVERT: E 104 MET cc_start: 0.9355 (ttt) cc_final: 0.9005 (ttt) REVERT: E 129 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8724 (mt) REVERT: E 232 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8188 (mmmt) REVERT: E 327 ARG cc_start: 0.7459 (mtm180) cc_final: 0.6977 (mtp180) REVERT: E 347 LYS cc_start: 0.8992 (tttp) cc_final: 0.8439 (tppt) REVERT: E 424 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8397 (mp) REVERT: E 428 GLN cc_start: 0.7941 (mm110) cc_final: 0.7396 (mm-40) REVERT: E 504 ARG cc_start: 0.7578 (mtm110) cc_final: 0.7292 (mtt90) REVERT: F 530 MET cc_start: 0.9264 (mtp) cc_final: 0.8973 (mtp) REVERT: O 23 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6737 (mpt90) REVERT: Q 85 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: P 76 TRP cc_start: 0.7635 (p-90) cc_final: 0.6881 (t60) REVERT: R 53 LYS cc_start: 0.8018 (mttt) cc_final: 0.7440 (mtmm) outliers start: 87 outliers final: 59 residues processed: 457 average time/residue: 0.6339 time to fit residues: 331.9557 Evaluate side-chains 460 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 391 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 TYR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain R residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 36 optimal weight: 0.8980 chunk 254 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 188 optimal weight: 0.0980 chunk 206 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 616 ASN I 95 GLN C 432 GLN D 616 ASN M 95 GLN K 56 GLN E 377 ASN Q 69 ASN Q 95 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.159501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.131945 restraints weight = 23630.759| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.41 r_work: 0.3045 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25335 Z= 0.129 Angle : 0.544 9.393 34533 Z= 0.276 Chirality : 0.044 0.260 3972 Planarity : 0.004 0.041 4290 Dihedral : 6.000 53.042 4758 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.76 % Allowed : 16.02 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 2973 helix: 0.87 (0.26), residues: 432 sheet: 0.23 (0.16), residues: 933 loop : -0.18 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 178 TYR 0.017 0.001 TYR R 49 PHE 0.014 0.001 PHE A 391 TRP 0.017 0.001 TRP K 50 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (25218) covalent geometry : angle 0.52283 / 0.27 (34227) SS BOND : bond 0.00313 / 0.21 ( 45) SS BOND : angle 0.83856 / 0.57 ( 90) hydrogen bonds : bond 0.03719 / 2.49 ( 663) hydrogen bonds : angle 5.02092 / 3.38 ( 1764) link_ALPHA1-3 : bond 0.01455 / 0.73 ( 3) link_ALPHA1-3 : angle 1.03595 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00127 / 0.06 ( 3) link_ALPHA1-6 : angle 2.19665 / 1.50 ( 9) link_BETA1-4 : bond 0.00477 / 0.29 ( 18) link_BETA1-4 : angle 1.79305 / 1.31 ( 54) link_NAG-ASN : bond 0.00218 / 0.13 ( 48) link_NAG-ASN : angle 2.02009 / 1.38 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 389 time to evaluate : 0.941 Fit side-chains REVERT: A 232 LYS cc_start: 0.8929 (mtmp) cc_final: 0.7973 (mmmt) REVERT: A 347 LYS cc_start: 0.9008 (tttp) cc_final: 0.8416 (tppt) REVERT: A 428 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7277 (mm-40) REVERT: A 479 TRP cc_start: 0.7692 (m-10) cc_final: 0.7367 (m-10) REVERT: G 97 MET cc_start: 0.9065 (ptm) cc_final: 0.8791 (ptm) REVERT: G 100 GLN cc_start: 0.9011 (mt0) cc_final: 0.8684 (mt0) REVERT: I 50 ASP cc_start: 0.8409 (m-30) cc_final: 0.8145 (m-30) REVERT: H 56 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: H 76 TRP cc_start: 0.7454 (p-90) cc_final: 0.7023 (t60) REVERT: H 100 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6292 (m-80) REVERT: L 45 LYS cc_start: 0.8242 (ttpp) cc_final: 0.8003 (ttpp) REVERT: L 53 LYS cc_start: 0.7976 (mttt) cc_final: 0.7311 (mtmm) REVERT: C 114 GLN cc_start: 0.7762 (tt0) cc_final: 0.7340 (tt0) REVERT: C 211 GLU cc_start: 0.8183 (tp30) cc_final: 0.7769 (tp30) REVERT: C 232 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8226 (mmpt) REVERT: C 267 GLU cc_start: 0.6822 (mp0) cc_final: 0.6557 (mp0) REVERT: C 340 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: C 347 LYS cc_start: 0.8958 (tttp) cc_final: 0.8519 (tppt) REVERT: C 426 MET cc_start: 0.8258 (tpt) cc_final: 0.7980 (tpp) REVERT: C 479 TRP cc_start: 0.7748 (m-10) cc_final: 0.6642 (m-10) REVERT: J 4 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8279 (mt) REVERT: K 23 GLU cc_start: 0.8250 (tt0) cc_final: 0.7591 (tp30) REVERT: K 54 TYR cc_start: 0.9053 (m-80) cc_final: 0.8783 (m-80) REVERT: K 100 ASP cc_start: 0.8322 (m-30) cc_final: 0.8007 (m-30) REVERT: N 45 LYS cc_start: 0.8084 (ttpp) cc_final: 0.7626 (tttt) REVERT: E 104 MET cc_start: 0.9357 (ttt) cc_final: 0.9014 (ttt) REVERT: E 129 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8658 (mt) REVERT: E 232 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8134 (mmmt) REVERT: E 327 ARG cc_start: 0.7507 (mtm180) cc_final: 0.7022 (mtp180) REVERT: E 347 LYS cc_start: 0.8976 (tttp) cc_final: 0.8431 (tppt) REVERT: E 424 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8382 (mp) REVERT: E 428 GLN cc_start: 0.7904 (mm110) cc_final: 0.7179 (mm-40) REVERT: E 504 ARG cc_start: 0.7542 (mtm110) cc_final: 0.7256 (mtt90) REVERT: F 530 MET cc_start: 0.9249 (mtp) cc_final: 0.8958 (mtp) REVERT: O 23 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6915 (mpt90) REVERT: O 46 GLU cc_start: 0.8524 (tt0) cc_final: 0.8263 (pt0) REVERT: Q 85 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7184 (m-30) REVERT: P 76 TRP cc_start: 0.7599 (p-90) cc_final: 0.6874 (t60) REVERT: R 53 LYS cc_start: 0.7950 (mttt) cc_final: 0.7383 (mtmm) outliers start: 72 outliers final: 47 residues processed: 441 average time/residue: 0.6266 time to fit residues: 316.6322 Evaluate side-chains 436 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 380 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain P residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 57 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 124 optimal weight: 0.0170 chunk 141 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 293 GLN B 616 ASN I 95 GLN C 293 GLN C 428 GLN C 432 GLN D 616 ASN M 95 GLN E 377 ASN Q 69 ASN Q 95 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.160343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.135059 restraints weight = 23695.565| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.30 r_work: 0.3088 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25335 Z= 0.104 Angle : 0.518 8.824 34533 Z= 0.262 Chirality : 0.043 0.246 3972 Planarity : 0.004 0.041 4290 Dihedral : 5.605 53.215 4758 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.03 % Allowed : 16.93 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 2973 helix: 1.11 (0.27), residues: 432 sheet: 0.29 (0.16), residues: 948 loop : -0.11 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 178 TYR 0.021 0.001 TYR C 173 PHE 0.013 0.001 PHE A 391 TRP 0.023 0.001 TRP C 427 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (25218) covalent geometry : angle 0.49777 / 0.26 (34227) SS BOND : bond 0.00267 / 0.18 ( 45) SS BOND : angle 0.75454 / 0.52 ( 90) hydrogen bonds : bond 0.03413 / 2.29 ( 663) hydrogen bonds : angle 4.91657 / 3.30 ( 1764) link_ALPHA1-3 : bond 0.01503 / 0.75 ( 3) link_ALPHA1-3 : angle 1.01477 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00037 / 0.02 ( 3) link_ALPHA1-6 : angle 2.06636 / 1.37 ( 9) link_BETA1-4 : bond 0.00467 / 0.28 ( 18) link_BETA1-4 : angle 1.68993 / 1.23 ( 54) link_NAG-ASN : bond 0.00179 / 0.11 ( 48) link_NAG-ASN : angle 1.89756 / 1.30 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 380 time to evaluate : 0.949 Fit side-chains REVERT: A 232 LYS cc_start: 0.8971 (mtmp) cc_final: 0.8193 (mmmt) REVERT: A 347 LYS cc_start: 0.8985 (tttp) cc_final: 0.8555 (tppt) REVERT: A 479 TRP cc_start: 0.7655 (m-10) cc_final: 0.7453 (m-10) REVERT: G 97 MET cc_start: 0.8960 (ptm) cc_final: 0.8758 (ptm) REVERT: G 100 GLN cc_start: 0.8820 (mt0) cc_final: 0.8476 (mt0) REVERT: I 50 ASP cc_start: 0.8415 (m-30) cc_final: 0.8147 (m-30) REVERT: H 56 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7668 (mp10) REVERT: H 76 TRP cc_start: 0.7492 (p-90) cc_final: 0.7131 (t60) REVERT: L 53 LYS cc_start: 0.7933 (mttt) cc_final: 0.7526 (mtmm) REVERT: C 114 GLN cc_start: 0.7749 (tt0) cc_final: 0.7363 (tt0) REVERT: C 211 GLU cc_start: 0.8127 (tp30) cc_final: 0.7801 (tp30) REVERT: C 232 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8420 (mmpt) REVERT: C 267 GLU cc_start: 0.6757 (mp0) cc_final: 0.6545 (mp0) REVERT: C 340 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: C 347 LYS cc_start: 0.8926 (tttp) cc_final: 0.8583 (tppt) REVERT: C 479 TRP cc_start: 0.7610 (m-10) cc_final: 0.6795 (m-10) REVERT: D 530 MET cc_start: 0.9097 (mtp) cc_final: 0.8868 (mtm) REVERT: J 91 TYR cc_start: 0.8895 (m-80) cc_final: 0.8624 (m-80) REVERT: K 23 GLU cc_start: 0.8090 (tt0) cc_final: 0.7608 (tp30) REVERT: K 54 TYR cc_start: 0.8939 (m-80) cc_final: 0.8733 (m-80) REVERT: K 100 ASP cc_start: 0.8207 (m-30) cc_final: 0.7937 (m-30) REVERT: N 45 LYS cc_start: 0.7950 (ttpp) cc_final: 0.7608 (tttt) REVERT: N 53 LYS cc_start: 0.7228 (mtmm) cc_final: 0.6960 (mttt) REVERT: E 104 MET cc_start: 0.9245 (ttt) cc_final: 0.8879 (ttt) REVERT: E 129 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8678 (mt) REVERT: E 232 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8216 (mmmt) REVERT: E 327 ARG cc_start: 0.7680 (mtm180) cc_final: 0.7218 (mtp180) REVERT: E 347 LYS cc_start: 0.8920 (tttp) cc_final: 0.8487 (tppt) REVERT: E 428 GLN cc_start: 0.7791 (mm110) cc_final: 0.7264 (mm-40) REVERT: E 504 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6907 (mtt90) REVERT: Q 85 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: P 76 TRP cc_start: 0.7599 (p-90) cc_final: 0.7028 (t60) REVERT: R 53 LYS cc_start: 0.7945 (mttt) cc_final: 0.7569 (mtmm) outliers start: 53 outliers final: 38 residues processed: 417 average time/residue: 0.6478 time to fit residues: 309.0404 Evaluate side-chains 411 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 368 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain P residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 230 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 168 optimal weight: 0.0870 chunk 119 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 108 optimal weight: 0.0020 chunk 267 optimal weight: 0.9990 chunk 48 optimal weight: 0.0570 chunk 160 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 616 ASN I 95 GLN C 432 GLN D 616 ASN J 3 GLN M 95 GLN N 52 ASN E 136 ASN E 293 GLN E 377 ASN Q 69 ASN Q 95 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.162175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.135345 restraints weight = 23682.409| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.37 r_work: 0.3053 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25335 Z= 0.094 Angle : 0.505 8.408 34533 Z= 0.256 Chirality : 0.043 0.241 3972 Planarity : 0.004 0.043 4290 Dihedral : 5.314 53.312 4758 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.69 % Allowed : 17.16 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 2973 helix: 1.28 (0.27), residues: 432 sheet: 0.39 (0.16), residues: 942 loop : -0.05 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 178 TYR 0.021 0.001 TYR C 173 PHE 0.011 0.001 PHE L 51 TRP 0.018 0.001 TRP K 50 HIS 0.002 0.000 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (25218) covalent geometry : angle 0.48619 / 0.25 (34227) SS BOND : bond 0.00256 / 0.17 ( 45) SS BOND : angle 0.71113 / 0.48 ( 90) hydrogen bonds : bond 0.03206 / 2.16 ( 663) hydrogen bonds : angle 4.83932 / 3.25 ( 1764) link_ALPHA1-3 : bond 0.01534 / 0.77 ( 3) link_ALPHA1-3 : angle 1.01058 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00090 / 0.05 ( 3) link_ALPHA1-6 : angle 1.92925 / 1.26 ( 9) link_BETA1-4 : bond 0.00467 / 0.28 ( 18) link_BETA1-4 : angle 1.62401 / 1.18 ( 54) link_NAG-ASN : bond 0.00160 / 0.10 ( 48) link_NAG-ASN : angle 1.81390 / 1.24 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9230.36 seconds wall clock time: 157 minutes 44.41 seconds (9464.41 seconds total)