Starting phenix.real_space_refine on Fri Sep 19 00:21:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8c_44342/09_2025/9b8c_44342.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8c_44342/09_2025/9b8c_44342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8c_44342/09_2025/9b8c_44342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8c_44342/09_2025/9b8c_44342.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8c_44342/09_2025/9b8c_44342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8c_44342/09_2025/9b8c_44342.cif" } resolution = 3.3 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= 0.024 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 128 5.16 5 C 13072 2.51 5 N 3502 2.21 5 O 4197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20899 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3321 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 2 Chain: "B" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 934 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3358 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 2 Chain: "D" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3330 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 18, 'TRANS': 403} Chain breaks: 2 Chain: "E" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 951 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "F" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 957 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" 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: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 999 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" 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: "J" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "K" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "L" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "M" 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: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 5.21, per 1000 atoms: 0.25 Number of scatterers: 20899 At special positions: 0 Unit cell: (125.28, 118.755, 180.09, 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 128 16.00 O 4197 8.00 N 3502 7.00 C 13072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 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 ALPHA1-2 " MAN O 4 " - " MAN O 5 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " ALPHA1-6 " BMA O 3 " - " MAN O 6 " " MAN O 6 " - " MAN O 8 " BETA1-3 " NAG O 1 " - " NAG O 2 " BETA1-4 " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A 601 " - " ASN A 156 " " NAG A 602 " - " ASN A 386 " " NAG A 603 " - " ASN A 392 " " NAG A 604 " - " ASN A 133 " " NAG A 605 " - " ASN A 88 " " NAG A 606 " - " ASN A 241 " " NAG A 607 " - " ASN A 234 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 332 " " NAG A 611 " - " ASN A 448 " " NAG A 612 " - " ASN A 289 " " NAG A 613 " - " ASN A 276 " " NAG A 614 " - " ASN A 355 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 301 " " NAG C 602 " - " ASN C 332 " " NAG C 603 " - " ASN C 295 " " NAG C 604 " - " ASN C 448 " " NAG C 605 " - " ASN C 386 " " NAG C 606 " - " ASN C 197 " " NAG C 607 " - " ASN C 234 " " NAG C 608 " - " ASN C 289 " " NAG C 609 " - " ASN C 88 " " NAG C 610 " - " ASN C 241 " " NAG C 611 " - " ASN C 133 " " NAG C 612 " - " ASN C 276 " " NAG D 601 " - " ASN D 301 " " NAG D 602 " - " ASN D 386 " " NAG D 603 " - " ASN D 332 " " NAG D 604 " - " ASN D 295 " " NAG D 605 " - " ASN D 276 " " NAG D 606 " - " ASN D 133 " " NAG D 607 " - " ASN D 88 " " NAG D 608 " - " ASN D 234 " " NAG D 609 " - " ASN D 289 " " NAG D 610 " - " ASN D 448 " " NAG D 611 " - " ASN D 241 " " NAG D 612 " - " ASN D 355 " " NAG D 613 " - " ASN D 392 " " NAG E 701 " - " ASN E 618 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 611 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN C 160 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN D 160 " " NAG V 1 " - " ASN D 197 " " NAG W 1 " - " ASN D 156 " " NAG X 1 " - " ASN D 262 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 898.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 42 sheets defined 19.8% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.315A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.902A pdb=" N ARG A 151 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.833A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.607A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.218A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.910A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.139A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 386 through 390 removed outlier: 4.054A pdb=" N GLY C 389 " --> pdb=" O ASN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.597A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.312A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 334 through 350 removed outlier: 5.639A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 476 through 484 removed outlier: 4.378A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.506A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 596 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 661 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.341A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.579A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 removed outlier: 3.501A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.652A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.578A pdb=" N ILE H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.025A pdb=" N GLU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.586A pdb=" N THR M 87 " --> pdb=" O ASP M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 27B through 31 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.277A 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: 4.605A 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 130 through 133 removed outlier: 3.578A pdb=" N PHE A 159 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.599A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, 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 307 removed outlier: 6.548A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 303 " --> pdb=" O GLY A 320 " (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 467 through 469 Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.072A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.618A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AB5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.547A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, 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 311 removed outlier: 6.608A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR C 303 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLN C 314 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 314 through 323 current: chain 'C' and resid 465 through 469 Processing sheet with id=AB8, first strand: chain 'C' and resid 374 through 375 Processing sheet with id=AB9, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.199A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.589A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AC5, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.577A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 311 removed outlier: 6.722A pdb=" N ASN D 301 " --> pdb=" O ILE D 322 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE D 322 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR D 303 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN D 314 " --> pdb=" O ILE D 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 314 through 323 current: chain 'D' and resid 414 through 419 Processing sheet with id=AC8, first strand: chain 'D' and resid 360 through 361 removed outlier: 6.714A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AD1, first strand: chain 'G' and resid 33 through 38 removed outlier: 6.428A pdb=" N TRP G 35 " --> pdb=" O MET G 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 48 current: chain 'G' and resid 95A through 98 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 46 through 51 removed outlier: 6.569A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AD5, first strand: chain 'I' and resid 34 through 40 removed outlier: 6.942A pdb=" N MET I 34 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100H through 103 Processing sheet with id=AD6, first strand: chain 'J' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 9 through 13 current: chain 'J' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 45 through 48 current: chain 'J' and resid 96 through 98 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AD8, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AD9, first strand: chain 'K' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 11 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 59 current: chain 'K' and resid 100H through 101 Processing sheet with id=AE1, first strand: chain 'L' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 11 current: chain 'L' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 46 current: chain 'L' and resid 95A through 98 No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE3, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'M' and resid 34 through 39 removed outlier: 7.009A pdb=" N MET M 34 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=AE5, first strand: chain 'N' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'N' and resid 18 through 24 572 hydrogen bonds defined for protein. 1488 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: 4.36 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6542 1.34 - 1.47: 5506 1.47 - 1.59: 9082 1.59 - 1.71: 1 1.71 - 1.84: 175 Bond restraints: 21306 Sorted by residual: bond pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " ideal model delta sigma weight residual 1.808 1.734 0.074 3.30e-02 9.18e+02 4.97e+00 bond pdb=" CB ILE D 420 " pdb=" CG2 ILE D 420 " ideal model delta sigma weight residual 1.521 1.575 -0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " ideal model delta sigma weight residual 1.513 1.555 -0.042 2.59e-02 1.49e+03 2.62e+00 bond pdb=" C LEU D 416 " pdb=" N PRO D 417 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.59e+00 bond pdb=" N TYR L 49 " pdb=" CA TYR L 49 " ideal model delta sigma weight residual 1.471 1.499 -0.028 1.74e-02 3.30e+03 2.57e+00 ... (remaining 21301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 28379 2.55 - 5.09: 470 5.09 - 7.64: 51 7.64 - 10.19: 3 10.19 - 12.73: 1 Bond angle restraints: 28904 Sorted by residual: angle pdb=" N GLU A 482 " pdb=" CA GLU A 482 " pdb=" C GLU A 482 " ideal model delta sigma weight residual 109.18 102.58 6.60 1.42e+00 4.96e-01 2.16e+01 angle pdb=" CA TYS H 100H" pdb=" CB TYS H 100H" pdb=" CG TYS H 100H" ideal model delta sigma weight residual 113.82 126.55 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 113.90 121.35 -7.45 1.80e+00 3.09e-01 1.71e+01 angle pdb=" N GLY D 379 " pdb=" CA GLY D 379 " pdb=" C GLY D 379 " ideal model delta sigma weight residual 113.18 104.11 9.07 2.37e+00 1.78e-01 1.46e+01 angle pdb=" N ARG L 54 " pdb=" CA ARG L 54 " pdb=" C ARG L 54 " ideal model delta sigma weight residual 109.81 118.07 -8.26 2.21e+00 2.05e-01 1.40e+01 ... (remaining 28899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.91: 13150 23.91 - 47.81: 396 47.81 - 71.72: 86 71.72 - 95.63: 24 95.63 - 119.53: 15 Dihedral angle restraints: 13671 sinusoidal: 6368 harmonic: 7303 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 43.07 49.93 1 1.00e+01 1.00e-02 3.42e+01 dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual 93.00 139.44 -46.44 1 1.00e+01 1.00e-02 2.98e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -132.11 46.11 1 1.00e+01 1.00e-02 2.95e+01 ... (remaining 13668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 3264 0.112 - 0.224: 181 0.224 - 0.336: 4 0.336 - 0.449: 1 0.449 - 0.561: 1 Chirality restraints: 3451 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 160 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" C1 NAG C 603 " pdb=" ND2 ASN C 295 " pdb=" C2 NAG C 603 " pdb=" O5 NAG C 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 386 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 3448 not shown) Planarity restraints: 3646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 66 " 0.236 9.50e-02 1.11e+02 1.06e-01 8.16e+00 pdb=" NE ARG H 66 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG H 66 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG H 66 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG H 66 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 374 " -0.014 2.00e-02 2.50e+03 2.26e-02 7.63e+00 pdb=" CG HIS C 374 " 0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS C 374 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 HIS C 374 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 HIS C 374 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS C 374 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 646 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.15e+00 pdb=" C LEU B 646 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU B 646 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU B 647 " 0.016 2.00e-02 2.50e+03 ... (remaining 3643 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1511 2.73 - 3.27: 19516 3.27 - 3.82: 33794 3.82 - 4.36: 42348 4.36 - 4.90: 71595 Nonbonded interactions: 168764 Sorted by model distance: nonbonded pdb=" O4 NAG O 1 " pdb=" N2 NAG O 2 " model vdw 2.190 3.120 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP E 632 " model vdw 2.202 3.120 nonbonded pdb=" NH1 ARG A 169 " pdb=" CE1 TYS H 100H" model vdw 2.240 3.420 nonbonded pdb=" O PHE I 29 " pdb=" NH2 ARG I 71 " model vdw 2.284 3.120 nonbonded pdb=" OD1 ASP A 107 " pdb=" NZ LYS B 574 " model vdw 2.287 3.120 ... (remaining 168759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 612) selection = (chain 'C' and (resid 33 through 56 or resid 83 through 612)) selection = (chain 'D' and (resid 33 through 56 or resid 83 through 612)) } ncs_group { reference = (chain 'B' and (resid 521 through 545 or resid 572 through 703)) selection = (chain 'E' and (resid 521 through 663 or resid 701 through 703)) selection = (chain 'F' and (resid 521 through 545 or resid 572 through 663 or resid 701 thro \ ugh 703)) } ncs_group { reference = chain 'G' selection = (chain 'J' and resid 3 through 106) selection = (chain 'N' and resid 3 through 106) } ncs_group { reference = chain 'I' selection = (chain 'K' and resid 2 through 111) selection = chain 'M' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'T' selection = chain 'X' } 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.090 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 0.074 21420 Z= 0.224 Angle : 0.894 16.510 29208 Z= 0.471 Chirality : 0.055 0.561 3451 Planarity : 0.005 0.106 3588 Dihedral : 12.611 119.533 8889 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.18 % Allowed : 2.59 % Favored : 97.23 % 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 aren not related in a simple way. whole: 0.11 (0.16), residues: 2507 helix: 0.73 (0.26), residues: 380 sheet: 0.35 (0.19), residues: 752 loop : -0.19 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG H 66 TYR 0.023 0.002 TYR E 638 PHE 0.043 0.004 PHE D 176 TRP 0.024 0.002 TRP D 479 HIS 0.030 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00522 (21306) covalent geometry : angle 0.86858 (28904) SS BOND : bond 0.00572 ( 38) SS BOND : angle 1.47461 ( 76) hydrogen bonds : bond 0.14077 ( 572) hydrogen bonds : angle 7.09886 ( 1488) link_ALPHA1-2 : bond 0.00961 ( 1) link_ALPHA1-2 : angle 2.29813 ( 3) link_ALPHA1-3 : bond 0.00317 ( 2) link_ALPHA1-3 : angle 1.67355 ( 6) link_ALPHA1-6 : bond 0.00349 ( 2) link_ALPHA1-6 : angle 1.66842 ( 6) link_BETA1-3 : bond 0.00003 ( 1) link_BETA1-3 : angle 11.84028 ( 3) link_BETA1-4 : bond 0.00617 ( 12) link_BETA1-4 : angle 2.43392 ( 36) link_NAG-ASN : bond 0.00402 ( 58) link_NAG-ASN : angle 1.98582 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 661 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8077 (mmm) cc_final: 0.7827 (mmm) REVERT: A 467 THR cc_start: 0.8123 (m) cc_final: 0.7880 (p) REVERT: B 648 GLU cc_start: 0.8001 (tp30) cc_final: 0.7736 (mm-30) REVERT: C 53 PHE cc_start: 0.7472 (m-80) cc_final: 0.7177 (m-10) REVERT: C 121 LYS cc_start: 0.8428 (mttt) cc_final: 0.8210 (mptt) REVERT: C 195 SER cc_start: 0.9073 (m) cc_final: 0.8467 (p) REVERT: C 303 THR cc_start: 0.8198 (m) cc_final: 0.7989 (m) REVERT: C 322 ILE cc_start: 0.7743 (mt) cc_final: 0.7519 (mm) REVERT: C 356 ASN cc_start: 0.8865 (m-40) cc_final: 0.8572 (m110) REVERT: D 106 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7883 (mt-10) REVERT: D 107 ASP cc_start: 0.8101 (t70) cc_final: 0.7821 (t0) REVERT: D 137 ASN cc_start: 0.7337 (m-40) cc_final: 0.7064 (m-40) REVERT: D 302 ASN cc_start: 0.7361 (m-40) cc_final: 0.7146 (p0) REVERT: D 340 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7549 (mp0) REVERT: D 443 ILE cc_start: 0.8786 (mm) cc_final: 0.8498 (mt) REVERT: D 467 THR cc_start: 0.7809 (m) cc_final: 0.7573 (m) REVERT: D 492 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7653 (mt-10) REVERT: E 599 SER cc_start: 0.9020 (t) cc_final: 0.8793 (p) REVERT: E 621 GLU cc_start: 0.8541 (pt0) cc_final: 0.7900 (pt0) REVERT: E 625 ASN cc_start: 0.8543 (m110) cc_final: 0.8204 (t0) REVERT: E 632 ASP cc_start: 0.8764 (t70) cc_final: 0.8132 (t0) REVERT: F 616 ASN cc_start: 0.7532 (p0) cc_final: 0.7159 (t0) REVERT: F 638 TYR cc_start: 0.8029 (m-80) cc_final: 0.7517 (m-80) REVERT: F 652 GLN cc_start: 0.8422 (mt0) cc_final: 0.8163 (mt0) REVERT: G 60 ASP cc_start: 0.8506 (p0) cc_final: 0.8179 (t0) REVERT: H 47 TRP cc_start: 0.8572 (t60) cc_final: 0.8003 (t60) REVERT: H 59 TYR cc_start: 0.7486 (m-80) cc_final: 0.6355 (m-80) REVERT: H 82 SER cc_start: 0.8725 (m) cc_final: 0.8367 (p) REVERT: H 100 SER cc_start: 0.7293 (m) cc_final: 0.7001 (p) REVERT: J 36 TYR cc_start: 0.9020 (m-80) cc_final: 0.8670 (m-80) REVERT: J 70 THR cc_start: 0.9220 (m) cc_final: 0.8969 (p) REVERT: J 79 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7172 (mt0) REVERT: J 85 ASP cc_start: 0.7726 (m-30) cc_final: 0.7401 (m-30) REVERT: K 12 VAL cc_start: 0.8858 (p) cc_final: 0.8655 (p) REVERT: L 31 ASN cc_start: 0.7831 (m-40) cc_final: 0.7485 (t0) REVERT: L 85 ASP cc_start: 0.6690 (m-30) cc_final: 0.6073 (m-30) REVERT: L 95 ASN cc_start: 0.8515 (m110) cc_final: 0.8251 (m-40) REVERT: M 13 GLN cc_start: 0.8194 (pm20) cc_final: 0.7862 (mm-40) REVERT: M 45 LEU cc_start: 0.7283 (tp) cc_final: 0.6754 (tp) REVERT: M 72 ASP cc_start: 0.7549 (t0) cc_final: 0.7285 (t0) REVERT: N 19 VAL cc_start: 0.8635 (m) cc_final: 0.8345 (p) REVERT: N 21 ILE cc_start: 0.8283 (mt) cc_final: 0.8080 (mt) REVERT: N 45 LYS cc_start: 0.7826 (tttt) cc_final: 0.7571 (ttpp) REVERT: N 47 MET cc_start: 0.7981 (mmm) cc_final: 0.7111 (mmm) outliers start: 4 outliers final: 0 residues processed: 663 average time/residue: 0.1737 time to fit residues: 171.8826 Evaluate side-chains 373 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 328 GLN A 432 GLN B 591 GLN D 33 ASN D 85 HIS E 540 GLN E 630 GLN F 630 GLN H 39 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 HIS K 82AHIS N 95 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102080 restraints weight = 34539.104| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.79 r_work: 0.3224 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21420 Z= 0.154 Angle : 0.668 13.403 29208 Z= 0.332 Chirality : 0.046 0.248 3451 Planarity : 0.004 0.039 3588 Dihedral : 9.275 105.288 4333 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.27 % Allowed : 9.90 % Favored : 87.83 % 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 aren not related in a simple way. whole: 0.28 (0.17), residues: 2507 helix: 1.61 (0.27), residues: 367 sheet: 0.40 (0.19), residues: 739 loop : -0.26 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 94 TYR 0.020 0.001 TYR L 49 PHE 0.018 0.002 PHE I 67 TRP 0.019 0.001 TRP A 479 HIS 0.008 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00345 (21306) covalent geometry : angle 0.63854 (28904) SS BOND : bond 0.00763 ( 38) SS BOND : angle 1.42742 ( 76) hydrogen bonds : bond 0.04138 ( 572) hydrogen bonds : angle 5.55629 ( 1488) link_ALPHA1-2 : bond 0.01664 ( 1) link_ALPHA1-2 : angle 2.01878 ( 3) link_ALPHA1-3 : bond 0.00515 ( 2) link_ALPHA1-3 : angle 1.83518 ( 6) link_ALPHA1-6 : bond 0.00386 ( 2) link_ALPHA1-6 : angle 2.19493 ( 6) link_BETA1-3 : bond 0.00005 ( 1) link_BETA1-3 : angle 9.17586 ( 3) link_BETA1-4 : bond 0.00405 ( 12) link_BETA1-4 : angle 1.99347 ( 36) link_NAG-ASN : bond 0.00423 ( 58) link_NAG-ASN : angle 1.91557 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 404 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 ASP cc_start: 0.7273 (p0) cc_final: 0.6968 (p0) REVERT: B 591 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: C 53 PHE cc_start: 0.7422 (m-80) cc_final: 0.6912 (m-10) REVERT: C 95 MET cc_start: 0.8875 (ptm) cc_final: 0.8614 (ptm) REVERT: C 107 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7945 (t0) REVERT: C 121 LYS cc_start: 0.8496 (mttt) cc_final: 0.8229 (mptt) REVERT: C 195 SER cc_start: 0.8957 (m) cc_final: 0.8295 (p) REVERT: C 213 ILE cc_start: 0.8917 (mt) cc_final: 0.8671 (tt) REVERT: C 356 ASN cc_start: 0.8904 (m-40) cc_final: 0.8627 (m110) REVERT: D 95 MET cc_start: 0.8439 (ptm) cc_final: 0.8157 (ptt) REVERT: D 106 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7544 (mt-10) REVERT: D 107 ASP cc_start: 0.8066 (t70) cc_final: 0.7733 (t0) REVERT: D 185 VAL cc_start: 0.8725 (t) cc_final: 0.8519 (p) REVERT: D 340 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7218 (mp0) REVERT: D 492 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7519 (mt-10) REVERT: E 592 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8614 (mp) REVERT: E 599 SER cc_start: 0.8974 (t) cc_final: 0.8757 (p) REVERT: E 625 ASN cc_start: 0.8555 (m110) cc_final: 0.8264 (t0) REVERT: E 632 ASP cc_start: 0.8431 (t70) cc_final: 0.7979 (t0) REVERT: E 647 GLU cc_start: 0.8380 (tt0) cc_final: 0.8099 (tt0) REVERT: F 616 ASN cc_start: 0.7769 (p0) cc_final: 0.7403 (t0) REVERT: F 638 TYR cc_start: 0.7644 (m-80) cc_final: 0.7271 (m-80) REVERT: F 652 GLN cc_start: 0.8424 (mt0) cc_final: 0.8181 (mt0) REVERT: H 58 ASN cc_start: 0.8074 (p0) cc_final: 0.7681 (p0) REVERT: H 59 TYR cc_start: 0.7536 (m-80) cc_final: 0.6600 (m-80) REVERT: I 66 ARG cc_start: 0.8457 (mtp180) cc_final: 0.8080 (ptp90) REVERT: I 86 ASP cc_start: 0.7618 (m-30) cc_final: 0.7356 (m-30) REVERT: J 36 TYR cc_start: 0.8914 (m-80) cc_final: 0.8412 (m-80) REVERT: J 70 THR cc_start: 0.9207 (m) cc_final: 0.8964 (p) REVERT: L 31 ASN cc_start: 0.8231 (m-40) cc_final: 0.7684 (t0) REVERT: L 47 MET cc_start: 0.7795 (mtp) cc_final: 0.7589 (mmm) REVERT: M 13 GLN cc_start: 0.8162 (pm20) cc_final: 0.7820 (mm-40) REVERT: M 72 ASP cc_start: 0.7427 (t0) cc_final: 0.7038 (t0) REVERT: N 19 VAL cc_start: 0.8577 (m) cc_final: 0.8191 (p) REVERT: N 21 ILE cc_start: 0.8377 (mt) cc_final: 0.8017 (mt) REVERT: N 45 LYS cc_start: 0.7683 (tttt) cc_final: 0.7334 (tttm) REVERT: N 103 ARG cc_start: 0.8621 (tpp80) cc_final: 0.8411 (tpp80) outliers start: 50 outliers final: 34 residues processed: 431 average time/residue: 0.1669 time to fit residues: 109.0734 Evaluate side-chains 380 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 36 TYR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 164 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 218 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 136 optimal weight: 0.3980 chunk 190 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.098266 restraints weight = 34961.576| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.84 r_work: 0.3162 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21420 Z= 0.186 Angle : 0.645 14.160 29208 Z= 0.320 Chirality : 0.046 0.286 3451 Planarity : 0.004 0.043 3588 Dihedral : 8.182 98.484 4333 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.77 % Allowed : 11.13 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 0.14 (0.17), residues: 2507 helix: 1.68 (0.28), residues: 361 sheet: 0.22 (0.19), residues: 744 loop : -0.35 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 103 TYR 0.014 0.001 TYR E 638 PHE 0.025 0.002 PHE A 391 TRP 0.022 0.002 TRP A 479 HIS 0.009 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00434 (21306) covalent geometry : angle 0.61426 (28904) SS BOND : bond 0.00570 ( 38) SS BOND : angle 1.34757 ( 76) hydrogen bonds : bond 0.03965 ( 572) hydrogen bonds : angle 5.24368 ( 1488) link_ALPHA1-2 : bond 0.01265 ( 1) link_ALPHA1-2 : angle 2.18044 ( 3) link_ALPHA1-3 : bond 0.00557 ( 2) link_ALPHA1-3 : angle 1.67911 ( 6) link_ALPHA1-6 : bond 0.00574 ( 2) link_ALPHA1-6 : angle 2.11557 ( 6) link_BETA1-3 : bond 0.00468 ( 1) link_BETA1-3 : angle 10.09891 ( 3) link_BETA1-4 : bond 0.00345 ( 12) link_BETA1-4 : angle 1.87714 ( 36) link_NAG-ASN : bond 0.00369 ( 58) link_NAG-ASN : angle 1.89362 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 364 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7697 (mmm160) REVERT: A 481 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.7919 (p) REVERT: B 543 ASN cc_start: 0.8560 (m-40) cc_final: 0.8256 (m-40) REVERT: C 53 PHE cc_start: 0.7624 (m-80) cc_final: 0.7373 (m-10) REVERT: C 95 MET cc_start: 0.8908 (ptm) cc_final: 0.8638 (ptm) REVERT: C 121 LYS cc_start: 0.8359 (mttt) cc_final: 0.8155 (mptt) REVERT: C 356 ASN cc_start: 0.8949 (m-40) cc_final: 0.8674 (m110) REVERT: D 106 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7419 (mt-10) REVERT: D 107 ASP cc_start: 0.8040 (t70) cc_final: 0.7718 (t0) REVERT: D 185 VAL cc_start: 0.8716 (t) cc_final: 0.8496 (p) REVERT: D 232 LYS cc_start: 0.9015 (mttt) cc_final: 0.8783 (mtmm) REVERT: D 340 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7207 (mp0) REVERT: D 452 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8000 (pp) REVERT: D 492 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7568 (mt-10) REVERT: E 592 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8717 (mp) REVERT: E 599 SER cc_start: 0.9071 (t) cc_final: 0.8789 (p) REVERT: E 625 ASN cc_start: 0.8609 (m110) cc_final: 0.8295 (t0) REVERT: E 632 ASP cc_start: 0.8569 (t70) cc_final: 0.8160 (t0) REVERT: E 647 GLU cc_start: 0.8438 (tt0) cc_final: 0.8157 (tt0) REVERT: F 616 ASN cc_start: 0.7726 (p0) cc_final: 0.7294 (t0) REVERT: F 638 TYR cc_start: 0.7762 (m-80) cc_final: 0.7345 (m-80) REVERT: H 46 GLU cc_start: 0.6951 (pm20) cc_final: 0.6581 (pm20) REVERT: H 47 TRP cc_start: 0.8586 (t60) cc_final: 0.7957 (t60) REVERT: H 59 TYR cc_start: 0.7700 (m-80) cc_final: 0.6639 (m-80) REVERT: H 100 GLU cc_start: 0.6736 (pp20) cc_final: 0.6516 (pp20) REVERT: I 83 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.7159 (mtm180) REVERT: L 27 ILE cc_start: 0.7884 (mm) cc_final: 0.7658 (mm) REVERT: L 31 ASN cc_start: 0.8319 (m-40) cc_final: 0.7879 (t0) REVERT: L 35 TRP cc_start: 0.6570 (m100) cc_final: 0.6165 (m100) REVERT: L 47 MET cc_start: 0.7788 (mtp) cc_final: 0.7587 (mmm) REVERT: L 95 ASN cc_start: 0.7866 (m-40) cc_final: 0.7464 (m-40) REVERT: M 13 GLN cc_start: 0.7943 (pm20) cc_final: 0.7557 (mm-40) REVERT: M 72 ASP cc_start: 0.7515 (t0) cc_final: 0.7157 (t0) REVERT: M 81 GLN cc_start: 0.8318 (tp40) cc_final: 0.8069 (tp40) REVERT: N 21 ILE cc_start: 0.8274 (mt) cc_final: 0.7938 (mt) REVERT: N 27 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6769 (p0) REVERT: N 45 LYS cc_start: 0.7570 (tttt) cc_final: 0.7201 (tttm) outliers start: 61 outliers final: 47 residues processed: 404 average time/residue: 0.1546 time to fit residues: 95.0417 Evaluate side-chains 386 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 335 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 36 TYR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 116 optimal weight: 0.6980 chunk 223 optimal weight: 7.9990 chunk 86 optimal weight: 0.0470 chunk 160 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 235 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099409 restraints weight = 34886.647| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.84 r_work: 0.3173 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21420 Z= 0.134 Angle : 0.588 13.748 29208 Z= 0.291 Chirality : 0.044 0.268 3451 Planarity : 0.003 0.041 3588 Dihedral : 7.262 97.114 4333 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.63 % Allowed : 12.44 % Favored : 84.92 % 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 aren not related in a simple way. whole: 0.09 (0.17), residues: 2507 helix: 1.70 (0.28), residues: 367 sheet: 0.08 (0.19), residues: 746 loop : -0.33 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.018 0.001 TYR J 49 PHE 0.025 0.002 PHE M 102 TRP 0.027 0.001 TRP A 479 HIS 0.008 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00305 (21306) covalent geometry : angle 0.55974 (28904) SS BOND : bond 0.00479 ( 38) SS BOND : angle 1.00815 ( 76) hydrogen bonds : bond 0.03495 ( 572) hydrogen bonds : angle 4.96761 ( 1488) link_ALPHA1-2 : bond 0.01235 ( 1) link_ALPHA1-2 : angle 2.40389 ( 3) link_ALPHA1-3 : bond 0.00925 ( 2) link_ALPHA1-3 : angle 1.55593 ( 6) link_ALPHA1-6 : bond 0.00245 ( 2) link_ALPHA1-6 : angle 2.01305 ( 6) link_BETA1-3 : bond 0.00769 ( 1) link_BETA1-3 : angle 9.64863 ( 3) link_BETA1-4 : bond 0.00380 ( 12) link_BETA1-4 : angle 1.71623 ( 36) link_NAG-ASN : bond 0.00306 ( 58) link_NAG-ASN : angle 1.75320 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 350 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7638 (mmm160) REVERT: C 53 PHE cc_start: 0.7634 (m-80) cc_final: 0.7141 (m-10) REVERT: C 95 MET cc_start: 0.8815 (ptm) cc_final: 0.8541 (ptm) REVERT: C 107 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7863 (t0) REVERT: C 188 TRP cc_start: 0.7282 (m100) cc_final: 0.6885 (m100) REVERT: C 280 ASN cc_start: 0.7174 (m-40) cc_final: 0.6957 (t0) REVERT: D 106 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7380 (mt-10) REVERT: D 107 ASP cc_start: 0.8055 (t70) cc_final: 0.7739 (t0) REVERT: D 185 VAL cc_start: 0.8682 (t) cc_final: 0.8449 (p) REVERT: D 232 LYS cc_start: 0.9052 (mttt) cc_final: 0.8828 (mtmm) REVERT: D 340 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7095 (mp0) REVERT: D 452 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7915 (pp) REVERT: D 492 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7561 (mt-10) REVERT: E 592 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8730 (mp) REVERT: E 599 SER cc_start: 0.9043 (t) cc_final: 0.8757 (p) REVERT: E 632 ASP cc_start: 0.8482 (t70) cc_final: 0.8116 (t0) REVERT: F 574 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7756 (mmtt) REVERT: F 616 ASN cc_start: 0.7788 (p0) cc_final: 0.7350 (t0) REVERT: F 638 TYR cc_start: 0.7732 (m-80) cc_final: 0.7278 (m-80) REVERT: G 105 THR cc_start: 0.6501 (m) cc_final: 0.6269 (p) REVERT: H 46 GLU cc_start: 0.6921 (pm20) cc_final: 0.6600 (pm20) REVERT: H 58 ASN cc_start: 0.7994 (p0) cc_final: 0.7673 (p0) REVERT: H 59 TYR cc_start: 0.7604 (m-80) cc_final: 0.6463 (m-80) REVERT: H 100 GLU cc_start: 0.6924 (pp20) cc_final: 0.6673 (pp20) REVERT: I 66 ARG cc_start: 0.8519 (mtp180) cc_final: 0.8296 (ptp90) REVERT: J 36 TYR cc_start: 0.8915 (m-80) cc_final: 0.8493 (m-80) REVERT: K 75 LYS cc_start: 0.8619 (pttt) cc_final: 0.8303 (pttm) REVERT: L 31 ASN cc_start: 0.8350 (m-40) cc_final: 0.7857 (t0) REVERT: L 35 TRP cc_start: 0.6708 (m100) cc_final: 0.6352 (m100) REVERT: L 47 MET cc_start: 0.7993 (mtp) cc_final: 0.7767 (mmm) REVERT: L 95 ASN cc_start: 0.7989 (m-40) cc_final: 0.7527 (m-40) REVERT: M 13 GLN cc_start: 0.7918 (pm20) cc_final: 0.7601 (mm-40) REVERT: M 72 ASP cc_start: 0.7737 (t0) cc_final: 0.7313 (t0) REVERT: M 81 GLN cc_start: 0.8431 (tp40) cc_final: 0.8198 (tp40) REVERT: N 31 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8398 (t0) REVERT: N 45 LYS cc_start: 0.7620 (tttt) cc_final: 0.7215 (tttm) outliers start: 58 outliers final: 40 residues processed: 388 average time/residue: 0.1531 time to fit residues: 90.3068 Evaluate side-chains 366 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 322 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 252 LYS Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 36 TYR Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 143 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.123895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095128 restraints weight = 34999.169| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.83 r_work: 0.3112 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21420 Z= 0.229 Angle : 0.662 14.109 29208 Z= 0.328 Chirality : 0.047 0.313 3451 Planarity : 0.004 0.041 3588 Dihedral : 7.016 95.913 4333 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.50 % Allowed : 12.17 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.13 (0.17), residues: 2507 helix: 1.54 (0.28), residues: 364 sheet: -0.11 (0.19), residues: 736 loop : -0.46 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 103 TYR 0.020 0.002 TYR G 49 PHE 0.020 0.002 PHE A 391 TRP 0.031 0.002 TRP A 479 HIS 0.009 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00538 (21306) covalent geometry : angle 0.63015 (28904) SS BOND : bond 0.00625 ( 38) SS BOND : angle 1.44231 ( 76) hydrogen bonds : bond 0.03939 ( 572) hydrogen bonds : angle 5.09143 ( 1488) link_ALPHA1-2 : bond 0.01214 ( 1) link_ALPHA1-2 : angle 2.29144 ( 3) link_ALPHA1-3 : bond 0.00673 ( 2) link_ALPHA1-3 : angle 1.57890 ( 6) link_ALPHA1-6 : bond 0.00361 ( 2) link_ALPHA1-6 : angle 1.99915 ( 6) link_BETA1-3 : bond 0.00929 ( 1) link_BETA1-3 : angle 10.74449 ( 3) link_BETA1-4 : bond 0.00292 ( 12) link_BETA1-4 : angle 1.67221 ( 36) link_NAG-ASN : bond 0.00415 ( 58) link_NAG-ASN : angle 1.94201 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 329 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8116 (p) REVERT: B 543 ASN cc_start: 0.8452 (m-40) cc_final: 0.8140 (m-40) REVERT: C 53 PHE cc_start: 0.7836 (m-80) cc_final: 0.7295 (m-10) REVERT: C 107 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8063 (t0) REVERT: D 106 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7407 (mt-10) REVERT: D 107 ASP cc_start: 0.8059 (t70) cc_final: 0.7789 (t0) REVERT: D 188 TRP cc_start: 0.7567 (m100) cc_final: 0.7342 (m100) REVERT: D 340 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7164 (mp0) REVERT: D 452 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8127 (pp) REVERT: D 492 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7571 (mt-10) REVERT: E 592 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8562 (mp) REVERT: E 599 SER cc_start: 0.9175 (t) cc_final: 0.8814 (p) REVERT: E 632 ASP cc_start: 0.8571 (t70) cc_final: 0.8127 (t0) REVERT: F 574 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7853 (mmtt) REVERT: F 616 ASN cc_start: 0.7844 (p0) cc_final: 0.7333 (t0) REVERT: F 638 TYR cc_start: 0.7891 (m-80) cc_final: 0.7408 (m-80) REVERT: G 32 TYR cc_start: 0.9012 (m-80) cc_final: 0.8487 (m-80) REVERT: G 105 THR cc_start: 0.6741 (m) cc_final: 0.6407 (p) REVERT: H 58 ASN cc_start: 0.8186 (p0) cc_final: 0.7947 (p0) REVERT: H 100 GLU cc_start: 0.6856 (pp20) cc_final: 0.6529 (pp20) REVERT: H 100 ASN cc_start: 0.8036 (p0) cc_final: 0.7740 (p0) REVERT: I 52 ASN cc_start: 0.8382 (t0) cc_final: 0.8135 (t0) REVERT: K 75 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8407 (pttm) REVERT: L 31 ASN cc_start: 0.8344 (m-40) cc_final: 0.7839 (t0) REVERT: L 35 TRP cc_start: 0.6485 (m100) cc_final: 0.6077 (m100) REVERT: L 53 LYS cc_start: 0.7078 (mttp) cc_final: 0.6592 (ttmt) REVERT: L 95 ASN cc_start: 0.8063 (m-40) cc_final: 0.7551 (m-40) REVERT: M 72 ASP cc_start: 0.7671 (t0) cc_final: 0.7362 (t0) REVERT: M 81 GLN cc_start: 0.8534 (tp40) cc_final: 0.8301 (tp40) REVERT: N 27 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6904 (p0) REVERT: N 45 LYS cc_start: 0.7621 (tttt) cc_final: 0.7169 (tttm) outliers start: 77 outliers final: 62 residues processed: 381 average time/residue: 0.1500 time to fit residues: 87.7488 Evaluate side-chains 373 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 305 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 36 TYR Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 169 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 195 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 191 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 591 GLN ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN E 585 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN G 38 GLN I 39 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN K 39 GLN N 31 ASN N 95 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.123804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095074 restraints weight = 35007.858| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.83 r_work: 0.3113 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21420 Z= 0.199 Angle : 0.633 13.722 29208 Z= 0.314 Chirality : 0.046 0.304 3451 Planarity : 0.004 0.038 3588 Dihedral : 6.648 96.352 4333 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.86 % Allowed : 12.31 % Favored : 83.83 % 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 aren not related in a simple way. whole: -0.27 (0.17), residues: 2507 helix: 1.53 (0.28), residues: 365 sheet: -0.28 (0.19), residues: 734 loop : -0.52 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 504 TYR 0.019 0.001 TYR J 49 PHE 0.021 0.002 PHE A 391 TRP 0.036 0.002 TRP A 479 HIS 0.007 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00467 (21306) covalent geometry : angle 0.60297 (28904) SS BOND : bond 0.00583 ( 38) SS BOND : angle 1.22584 ( 76) hydrogen bonds : bond 0.03754 ( 572) hydrogen bonds : angle 4.98541 ( 1488) link_ALPHA1-2 : bond 0.01154 ( 1) link_ALPHA1-2 : angle 2.28884 ( 3) link_ALPHA1-3 : bond 0.00884 ( 2) link_ALPHA1-3 : angle 1.59947 ( 6) link_ALPHA1-6 : bond 0.00048 ( 2) link_ALPHA1-6 : angle 1.79326 ( 6) link_BETA1-3 : bond 0.01505 ( 1) link_BETA1-3 : angle 10.50033 ( 3) link_BETA1-4 : bond 0.00347 ( 12) link_BETA1-4 : angle 1.52277 ( 36) link_NAG-ASN : bond 0.00342 ( 58) link_NAG-ASN : angle 1.89775 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 319 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8241 (p) REVERT: B 543 ASN cc_start: 0.8476 (m-40) cc_final: 0.8181 (m-40) REVERT: B 647 GLU cc_start: 0.8414 (tt0) cc_final: 0.8156 (tt0) REVERT: C 53 PHE cc_start: 0.7823 (m-80) cc_final: 0.7288 (m-10) REVERT: C 107 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8074 (t0) REVERT: D 106 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7397 (mt-10) REVERT: D 107 ASP cc_start: 0.8081 (t70) cc_final: 0.7796 (t0) REVERT: D 188 TRP cc_start: 0.7643 (m100) cc_final: 0.7424 (m100) REVERT: D 340 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7104 (mp0) REVERT: D 452 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8061 (pp) REVERT: D 492 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7602 (mt-10) REVERT: E 592 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8632 (mp) REVERT: E 599 SER cc_start: 0.9150 (t) cc_final: 0.8753 (p) REVERT: E 632 ASP cc_start: 0.8506 (t70) cc_final: 0.8179 (t0) REVERT: F 574 LYS cc_start: 0.8313 (mtmm) cc_final: 0.7884 (mmtt) REVERT: F 616 ASN cc_start: 0.7874 (p0) cc_final: 0.7307 (t0) REVERT: F 638 TYR cc_start: 0.7906 (m-80) cc_final: 0.7383 (m-80) REVERT: H 58 ASN cc_start: 0.8140 (p0) cc_final: 0.7872 (p0) REVERT: H 72 ASP cc_start: 0.7714 (t0) cc_final: 0.7394 (m-30) REVERT: H 100 ASN cc_start: 0.8256 (p0) cc_final: 0.7989 (p0) REVERT: I 52 ASN cc_start: 0.8516 (t0) cc_final: 0.8251 (t0) REVERT: J 103 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8394 (tpp80) REVERT: K 75 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8370 (pttm) REVERT: L 31 ASN cc_start: 0.8357 (m-40) cc_final: 0.7824 (t0) REVERT: L 35 TRP cc_start: 0.6780 (m100) cc_final: 0.6326 (m100) REVERT: L 47 MET cc_start: 0.7339 (mmm) cc_final: 0.6885 (mmm) REVERT: L 95 ASN cc_start: 0.8122 (m-40) cc_final: 0.7616 (m-40) REVERT: M 13 GLN cc_start: 0.7868 (pm20) cc_final: 0.7380 (mm-40) REVERT: M 72 ASP cc_start: 0.7648 (t0) cc_final: 0.7313 (t0) REVERT: M 81 GLN cc_start: 0.8562 (tp40) cc_final: 0.8293 (tp40) REVERT: N 27 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7063 (p0) REVERT: N 45 LYS cc_start: 0.7678 (tttt) cc_final: 0.7378 (tttm) outliers start: 85 outliers final: 65 residues processed: 374 average time/residue: 0.1505 time to fit residues: 87.1435 Evaluate side-chains 376 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 305 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 36 TYR Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain N residue 95 GLN Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 147 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN G 17 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099626 restraints weight = 33629.886| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.41 r_work: 0.3164 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21420 Z= 0.224 Angle : 0.658 13.470 29208 Z= 0.325 Chirality : 0.046 0.315 3451 Planarity : 0.004 0.039 3588 Dihedral : 6.595 95.764 4333 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.95 % Allowed : 13.03 % Favored : 83.02 % 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 aren not related in a simple way. whole: -0.39 (0.17), residues: 2507 helix: 1.46 (0.28), residues: 365 sheet: -0.42 (0.18), residues: 754 loop : -0.57 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 476 TYR 0.018 0.002 TYR G 49 PHE 0.017 0.002 PHE J 62 TRP 0.039 0.002 TRP A 479 HIS 0.007 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00527 (21306) covalent geometry : angle 0.62809 (28904) SS BOND : bond 0.00598 ( 38) SS BOND : angle 1.24159 ( 76) hydrogen bonds : bond 0.03842 ( 572) hydrogen bonds : angle 5.01389 ( 1488) link_ALPHA1-2 : bond 0.00934 ( 1) link_ALPHA1-2 : angle 2.14991 ( 3) link_ALPHA1-3 : bond 0.00606 ( 2) link_ALPHA1-3 : angle 1.62972 ( 6) link_ALPHA1-6 : bond 0.00040 ( 2) link_ALPHA1-6 : angle 1.70987 ( 6) link_BETA1-3 : bond 0.01437 ( 1) link_BETA1-3 : angle 10.48066 ( 3) link_BETA1-4 : bond 0.00345 ( 12) link_BETA1-4 : angle 1.55027 ( 36) link_NAG-ASN : bond 0.00382 ( 58) link_NAG-ASN : angle 1.97099 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 326 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8430 (p) REVERT: C 53 PHE cc_start: 0.7782 (m-80) cc_final: 0.7426 (m-10) REVERT: C 107 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8349 (t0) REVERT: D 106 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7923 (mt-10) REVERT: D 107 ASP cc_start: 0.8447 (t70) cc_final: 0.8222 (t0) REVERT: D 188 TRP cc_start: 0.7696 (m100) cc_final: 0.7465 (m100) REVERT: D 340 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7153 (mp0) REVERT: D 452 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8292 (pp) REVERT: D 492 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7904 (mt-10) REVERT: E 592 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8771 (mp) REVERT: E 632 ASP cc_start: 0.8527 (t70) cc_final: 0.8101 (t0) REVERT: F 574 LYS cc_start: 0.8350 (mtmm) cc_final: 0.8060 (mmtt) REVERT: F 616 ASN cc_start: 0.7863 (p0) cc_final: 0.7356 (t0) REVERT: F 638 TYR cc_start: 0.8039 (m-80) cc_final: 0.7569 (m-80) REVERT: G 17 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6926 (pm20) REVERT: G 105 THR cc_start: 0.7122 (m) cc_final: 0.6727 (p) REVERT: H 58 ASN cc_start: 0.8275 (p0) cc_final: 0.7967 (p0) REVERT: H 72 ASP cc_start: 0.7766 (t0) cc_final: 0.7458 (m-30) REVERT: H 100 ASN cc_start: 0.8516 (p0) cc_final: 0.8315 (p0) REVERT: I 52 ASN cc_start: 0.8595 (t0) cc_final: 0.8366 (t0) REVERT: I 64 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8203 (mmtt) REVERT: L 31 ASN cc_start: 0.8407 (m-40) cc_final: 0.7888 (t0) REVERT: L 35 TRP cc_start: 0.6927 (m100) cc_final: 0.6548 (m100) REVERT: L 46 LEU cc_start: 0.8627 (tp) cc_final: 0.8376 (tp) REVERT: L 47 MET cc_start: 0.7458 (mmm) cc_final: 0.7077 (mmm) REVERT: L 69 ASN cc_start: 0.8455 (t0) cc_final: 0.8251 (t0) REVERT: L 95 ASN cc_start: 0.8141 (m-40) cc_final: 0.7681 (m-40) REVERT: M 72 ASP cc_start: 0.7851 (t0) cc_final: 0.7593 (t0) REVERT: N 27 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7438 (p0) REVERT: N 45 LYS cc_start: 0.8091 (tttt) cc_final: 0.7873 (tttm) outliers start: 87 outliers final: 71 residues processed: 385 average time/residue: 0.1491 time to fit residues: 88.6407 Evaluate side-chains 388 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 311 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 36 TYR Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 240 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.122817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095891 restraints weight = 34167.448| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.64 r_work: 0.3117 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21420 Z= 0.177 Angle : 0.624 13.160 29208 Z= 0.309 Chirality : 0.045 0.304 3451 Planarity : 0.004 0.039 3588 Dihedral : 6.466 95.830 4333 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.59 % Allowed : 13.85 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.38 (0.17), residues: 2507 helix: 1.57 (0.28), residues: 365 sheet: -0.42 (0.19), residues: 739 loop : -0.60 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 504 TYR 0.018 0.001 TYR G 49 PHE 0.018 0.002 PHE A 391 TRP 0.040 0.002 TRP A 479 HIS 0.007 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00417 (21306) covalent geometry : angle 0.59164 (28904) SS BOND : bond 0.00534 ( 38) SS BOND : angle 1.58148 ( 76) hydrogen bonds : bond 0.03641 ( 572) hydrogen bonds : angle 4.91605 ( 1488) link_ALPHA1-2 : bond 0.01320 ( 1) link_ALPHA1-2 : angle 2.39614 ( 3) link_ALPHA1-3 : bond 0.00870 ( 2) link_ALPHA1-3 : angle 1.56766 ( 6) link_ALPHA1-6 : bond 0.00155 ( 2) link_ALPHA1-6 : angle 1.66158 ( 6) link_BETA1-3 : bond 0.01478 ( 1) link_BETA1-3 : angle 10.10438 ( 3) link_BETA1-4 : bond 0.00359 ( 12) link_BETA1-4 : angle 1.50111 ( 36) link_NAG-ASN : bond 0.00323 ( 58) link_NAG-ASN : angle 1.89522 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 319 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8308 (p) REVERT: C 53 PHE cc_start: 0.7921 (m-80) cc_final: 0.7415 (m-10) REVERT: C 107 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8303 (t0) REVERT: C 188 TRP cc_start: 0.7299 (m100) cc_final: 0.6585 (m-10) REVERT: D 106 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7660 (mt-10) REVERT: D 107 ASP cc_start: 0.8342 (t70) cc_final: 0.8069 (t0) REVERT: D 188 TRP cc_start: 0.7742 (m100) cc_final: 0.7462 (m100) REVERT: D 340 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7163 (mp0) REVERT: D 452 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8198 (pp) REVERT: D 492 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7763 (mt-10) REVERT: E 592 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8726 (mp) REVERT: F 574 LYS cc_start: 0.8347 (mtmm) cc_final: 0.7948 (mmtt) REVERT: F 616 ASN cc_start: 0.8166 (p0) cc_final: 0.7516 (t0) REVERT: G 17 GLN cc_start: 0.7300 (pm20) cc_final: 0.7092 (pm20) REVERT: G 105 THR cc_start: 0.7034 (m) cc_final: 0.6626 (p) REVERT: H 58 ASN cc_start: 0.8254 (p0) cc_final: 0.7957 (p0) REVERT: H 72 ASP cc_start: 0.7797 (t0) cc_final: 0.7433 (m-30) REVERT: H 100 ASN cc_start: 0.8442 (p0) cc_final: 0.8214 (p0) REVERT: I 52 ASN cc_start: 0.8699 (t0) cc_final: 0.8460 (t0) REVERT: I 64 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8182 (mmtt) REVERT: J 8 PRO cc_start: 0.8616 (Cg_exo) cc_final: 0.8388 (Cg_endo) REVERT: K 75 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7946 (pttm) REVERT: L 31 ASN cc_start: 0.8429 (m-40) cc_final: 0.7841 (t0) REVERT: L 35 TRP cc_start: 0.6825 (m100) cc_final: 0.6380 (m100) REVERT: L 46 LEU cc_start: 0.8474 (tp) cc_final: 0.8274 (tp) REVERT: L 47 MET cc_start: 0.7414 (mmm) cc_final: 0.6983 (mmm) REVERT: L 95 ASN cc_start: 0.8152 (m-40) cc_final: 0.7664 (m-40) REVERT: M 13 GLN cc_start: 0.8041 (pm20) cc_final: 0.7463 (mm-40) REVERT: M 72 ASP cc_start: 0.7814 (t0) cc_final: 0.7459 (t0) REVERT: N 27 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7210 (p0) REVERT: N 45 LYS cc_start: 0.7838 (tttt) cc_final: 0.7550 (tttm) outliers start: 79 outliers final: 67 residues processed: 373 average time/residue: 0.1643 time to fit residues: 94.1810 Evaluate side-chains 375 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 302 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 36 TYR Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 103 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 225 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 232 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.137749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.112002 restraints weight = 34357.386| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.57 r_work: 0.3400 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21420 Z= 0.149 Angle : 0.606 12.973 29208 Z= 0.300 Chirality : 0.045 0.295 3451 Planarity : 0.004 0.040 3588 Dihedral : 6.237 94.183 4333 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.91 % Allowed : 14.71 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.31 (0.17), residues: 2507 helix: 1.75 (0.29), residues: 361 sheet: -0.40 (0.19), residues: 739 loop : -0.57 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 504 TYR 0.020 0.001 TYR G 49 PHE 0.014 0.001 PHE A 391 TRP 0.037 0.001 TRP A 479 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00349 (21306) covalent geometry : angle 0.57691 (28904) SS BOND : bond 0.00523 ( 38) SS BOND : angle 1.36245 ( 76) hydrogen bonds : bond 0.03516 ( 572) hydrogen bonds : angle 4.78691 ( 1488) link_ALPHA1-2 : bond 0.01216 ( 1) link_ALPHA1-2 : angle 2.49817 ( 3) link_ALPHA1-3 : bond 0.00881 ( 2) link_ALPHA1-3 : angle 1.55965 ( 6) link_ALPHA1-6 : bond 0.00257 ( 2) link_ALPHA1-6 : angle 1.57713 ( 6) link_BETA1-3 : bond 0.01516 ( 1) link_BETA1-3 : angle 9.88403 ( 3) link_BETA1-4 : bond 0.00372 ( 12) link_BETA1-4 : angle 1.46360 ( 36) link_NAG-ASN : bond 0.00297 ( 58) link_NAG-ASN : angle 1.79833 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 321 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8428 (p) REVERT: C 53 PHE cc_start: 0.7842 (m-80) cc_final: 0.7487 (m-10) REVERT: C 107 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8284 (t0) REVERT: C 188 TRP cc_start: 0.7323 (m100) cc_final: 0.6692 (m100) REVERT: D 106 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7977 (mt-10) REVERT: D 107 ASP cc_start: 0.8440 (t70) cc_final: 0.8207 (t0) REVERT: D 187 LEU cc_start: 0.8737 (tp) cc_final: 0.8352 (tp) REVERT: D 188 TRP cc_start: 0.7652 (m100) cc_final: 0.7174 (m100) REVERT: D 340 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7120 (mp0) REVERT: D 452 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8242 (pp) REVERT: D 492 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7812 (mt-10) REVERT: E 592 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8864 (mp) REVERT: F 616 ASN cc_start: 0.7978 (p0) cc_final: 0.7398 (t0) REVERT: F 652 GLN cc_start: 0.8609 (mt0) cc_final: 0.8270 (mt0) REVERT: H 58 ASN cc_start: 0.8194 (p0) cc_final: 0.7865 (p0) REVERT: H 72 ASP cc_start: 0.7822 (t0) cc_final: 0.7455 (m-30) REVERT: H 100 ASN cc_start: 0.8541 (p0) cc_final: 0.8308 (p0) REVERT: I 52 ASN cc_start: 0.8560 (t0) cc_final: 0.8339 (t0) REVERT: I 64 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8163 (mmtt) REVERT: J 8 PRO cc_start: 0.8632 (Cg_exo) cc_final: 0.8431 (Cg_endo) REVERT: J 36 TYR cc_start: 0.9015 (m-80) cc_final: 0.8565 (m-80) REVERT: J 53 GLN cc_start: 0.7971 (tp-100) cc_final: 0.7563 (tp-100) REVERT: K 75 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8009 (pttm) REVERT: L 31 ASN cc_start: 0.8404 (m-40) cc_final: 0.7854 (t0) REVERT: L 35 TRP cc_start: 0.6767 (m100) cc_final: 0.6255 (m100) REVERT: L 47 MET cc_start: 0.7342 (mmm) cc_final: 0.7027 (mmm) REVERT: L 95 ASN cc_start: 0.8002 (m-40) cc_final: 0.7536 (m-40) REVERT: M 13 GLN cc_start: 0.7934 (pm20) cc_final: 0.7481 (mm-40) REVERT: M 72 ASP cc_start: 0.7829 (t0) cc_final: 0.7535 (t0) REVERT: N 27 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7322 (p0) REVERT: N 45 LYS cc_start: 0.8001 (tttt) cc_final: 0.7793 (tttm) outliers start: 64 outliers final: 57 residues processed: 365 average time/residue: 0.1507 time to fit residues: 85.6955 Evaluate side-chains 375 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 312 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 36 TYR Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 18 optimal weight: 0.4980 chunk 238 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 216 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 48 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 214 optimal weight: 0.8980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 625 ASN ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82AHIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.140093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114548 restraints weight = 34524.005| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.56 r_work: 0.3439 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21420 Z= 0.107 Angle : 0.566 12.621 29208 Z= 0.281 Chirality : 0.044 0.276 3451 Planarity : 0.004 0.051 3588 Dihedral : 5.839 91.589 4333 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.27 % Allowed : 15.12 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.17 (0.17), residues: 2507 helix: 1.93 (0.29), residues: 360 sheet: -0.33 (0.19), residues: 740 loop : -0.47 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 504 TYR 0.020 0.001 TYR G 49 PHE 0.010 0.001 PHE D 176 TRP 0.032 0.001 TRP A 479 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00245 (21306) covalent geometry : angle 0.53934 (28904) SS BOND : bond 0.00429 ( 38) SS BOND : angle 1.16253 ( 76) hydrogen bonds : bond 0.03141 ( 572) hydrogen bonds : angle 4.58492 ( 1488) link_ALPHA1-2 : bond 0.01205 ( 1) link_ALPHA1-2 : angle 2.82086 ( 3) link_ALPHA1-3 : bond 0.00911 ( 2) link_ALPHA1-3 : angle 1.41555 ( 6) link_ALPHA1-6 : bond 0.00425 ( 2) link_ALPHA1-6 : angle 1.46875 ( 6) link_BETA1-3 : bond 0.01549 ( 1) link_BETA1-3 : angle 9.40170 ( 3) link_BETA1-4 : bond 0.00437 ( 12) link_BETA1-4 : angle 1.40433 ( 36) link_NAG-ASN : bond 0.00275 ( 58) link_NAG-ASN : angle 1.63034 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 329 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ASN cc_start: 0.7890 (m-40) cc_final: 0.7688 (m-40) REVERT: B 634 GLU cc_start: 0.8104 (tt0) cc_final: 0.7879 (tt0) REVERT: C 53 PHE cc_start: 0.7836 (m-80) cc_final: 0.7482 (m-10) REVERT: C 107 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8125 (t0) REVERT: C 188 TRP cc_start: 0.7466 (m100) cc_final: 0.6810 (m-10) REVERT: C 217 TYR cc_start: 0.8013 (m-80) cc_final: 0.7486 (m-80) REVERT: D 106 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7883 (mt-10) REVERT: D 112 TRP cc_start: 0.8302 (t-100) cc_final: 0.7997 (t-100) REVERT: D 188 TRP cc_start: 0.7611 (m100) cc_final: 0.7214 (m100) REVERT: D 416 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7077 (mt) REVERT: D 452 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8141 (pp) REVERT: D 492 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7772 (mt-10) REVERT: E 592 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8874 (mp) REVERT: F 616 ASN cc_start: 0.7868 (p0) cc_final: 0.7368 (t0) REVERT: F 652 GLN cc_start: 0.8563 (mt0) cc_final: 0.8210 (mt0) REVERT: G 105 THR cc_start: 0.6994 (m) cc_final: 0.6635 (p) REVERT: H 47 TRP cc_start: 0.8626 (t60) cc_final: 0.8132 (t60) REVERT: H 72 ASP cc_start: 0.7791 (t0) cc_final: 0.7343 (m-30) REVERT: H 100 ASN cc_start: 0.8554 (p0) cc_final: 0.8334 (p0) REVERT: I 52 ASN cc_start: 0.8422 (t0) cc_final: 0.8220 (t0) REVERT: I 64 LYS cc_start: 0.8314 (mmtt) cc_final: 0.8112 (mmtt) REVERT: J 36 TYR cc_start: 0.8968 (m-80) cc_final: 0.8558 (m-80) REVERT: J 53 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7555 (tp-100) REVERT: K 75 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7948 (pttm) REVERT: L 31 ASN cc_start: 0.8368 (m-40) cc_final: 0.7853 (t0) REVERT: L 35 TRP cc_start: 0.6875 (m100) cc_final: 0.6332 (m100) REVERT: L 47 MET cc_start: 0.7444 (mmm) cc_final: 0.7136 (mmm) REVERT: L 95 ASN cc_start: 0.7898 (m-40) cc_final: 0.7461 (m-40) REVERT: M 13 GLN cc_start: 0.7886 (pm20) cc_final: 0.7484 (mm-40) REVERT: M 46 GLU cc_start: 0.8247 (tt0) cc_final: 0.7877 (pt0) REVERT: M 102 PHE cc_start: 0.6338 (t80) cc_final: 0.6091 (t80) REVERT: N 27 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7522 (p0) REVERT: N 45 LYS cc_start: 0.7893 (tttt) cc_final: 0.7671 (tttm) outliers start: 50 outliers final: 38 residues processed: 366 average time/residue: 0.1510 time to fit residues: 84.9875 Evaluate side-chains 352 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 308 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 36 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 13 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 244 optimal weight: 0.0270 chunk 0 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.138744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113342 restraints weight = 34477.699| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.54 r_work: 0.3418 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21420 Z= 0.143 Angle : 0.586 12.729 29208 Z= 0.290 Chirality : 0.044 0.292 3451 Planarity : 0.004 0.053 3588 Dihedral : 5.850 90.986 4333 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 2.41 % Allowed : 15.30 % Favored : 82.29 % 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 aren not related in a simple way. whole: -0.19 (0.17), residues: 2507 helix: 2.01 (0.29), residues: 355 sheet: -0.36 (0.19), residues: 759 loop : -0.50 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 103 TYR 0.021 0.001 TYR G 49 PHE 0.011 0.001 PHE J 62 TRP 0.036 0.001 TRP A 479 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00336 (21306) covalent geometry : angle 0.55765 (28904) SS BOND : bond 0.00472 ( 38) SS BOND : angle 1.23856 ( 76) hydrogen bonds : bond 0.03309 ( 572) hydrogen bonds : angle 4.59939 ( 1488) link_ALPHA1-2 : bond 0.01360 ( 1) link_ALPHA1-2 : angle 2.71884 ( 3) link_ALPHA1-3 : bond 0.00714 ( 2) link_ALPHA1-3 : angle 1.44015 ( 6) link_ALPHA1-6 : bond 0.00262 ( 2) link_ALPHA1-6 : angle 1.54645 ( 6) link_BETA1-3 : bond 0.01434 ( 1) link_BETA1-3 : angle 9.73837 ( 3) link_BETA1-4 : bond 0.00360 ( 12) link_BETA1-4 : angle 1.45353 ( 36) link_NAG-ASN : bond 0.00302 ( 58) link_NAG-ASN : angle 1.71393 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5356.15 seconds wall clock time: 92 minutes 36.28 seconds (5556.28 seconds total)