Starting phenix.real_space_refine on Sun Sep 13 01:04:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x9s_22109/09_2026/6x9s_22109.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x9s_22109/09_2026/6x9s_22109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x9s_22109/09_2026/6x9s_22109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x9s_22109/09_2026/6x9s_22109.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6x9s_22109/09_2026/6x9s_22109.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x9s_22109/09_2026/6x9s_22109.cif" model { file = "/net/cci-nas-00/data/ceres_data/6x9s_22109/09_2026/6x9s_22109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x9s_22109/09_2026/6x9s_22109.cif" } resolution = 3.1 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= 0.007 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 126 5.16 5 C 12258 2.51 5 N 3273 2.21 5 O 3933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19590 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 chiralities: 13 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 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 chiralities: 2 Chain: "I" 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 chiralities: 13 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "T" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "U" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "V" 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: "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 chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "0" 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 chiralities: 2 Chain: "S" 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 chiralities: 13 Chain: "T" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.36, per 1000 atoms: 0.22 Number of scatterers: 19590 At special positions: 0 Unit cell: (122.57, 127.72, 150.38, 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 126 16.00 O 3933 8.00 N 3273 7.00 C 12258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 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=2.02 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=2.14 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.11 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.06 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.14 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.11 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 119 " - pdb=" SG CYS S 205 " distance=2.06 Simple disulfide: pdb=" SG CYS S 126 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 157 " distance=2.02 Simple disulfide: pdb=" SG CYS S 218 " - pdb=" SG CYS S 247 " distance=2.03 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.14 Simple disulfide: pdb=" SG CYS S 296 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS S 378 " - pdb=" SG CYS S 445 " distance=2.02 Simple disulfide: pdb=" SG CYS S 385 " - pdb=" SG CYS S 418 " distance=2.02 Simple disulfide: pdb=" SG CYS S 501 " - pdb=" SG CYS T 605 " distance=2.11 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.02 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.04 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG 0 1 " - " ASN S 448 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 606 " - " ASN A 160 " " NAG A 609 " - " ASN A 234 " " NAG A 614 " - " ASN A 276 " " NAG A 615 " - " ASN A 295 " " NAG A 616 " - " ASN A 301 " " NAG A 617 " - " ASN A 332 " " NAG A 618 " - " ASN A 339 " " NAG A 619 " - " ASN A 355 " " NAG A 620 " - " ASN A 363 " " NAG A 623 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 1 " - " ASN A 156 " " NAG D 1 " - " ASN A 197 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN A 448 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 137 " " NAG I 606 " - " ASN I 160 " " NAG I 609 " - " ASN I 234 " " NAG I 614 " - " ASN I 276 " " NAG I 615 " - " ASN I 295 " " NAG I 616 " - " ASN I 301 " " NAG I 617 " - " ASN I 332 " " NAG I 618 " - " ASN I 339 " " NAG I 619 " - " ASN I 355 " " NAG I 620 " - " ASN I 363 " " NAG I 623 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG J 703 " - " ASN J 625 " " NAG J 704 " - " ASN J 637 " " NAG N 1 " - " ASN I 156 " " NAG O 1 " - " ASN I 197 " " NAG P 1 " - " ASN I 262 " " NAG Q 1 " - " ASN I 386 " " NAG R 1 " - " ASN I 448 " " NAG S 601 " - " ASN S 88 " " NAG S 602 " - " ASN S 133 " " NAG S 603 " - " ASN S 137 " " NAG S 606 " - " ASN S 160 " " NAG S 609 " - " ASN S 234 " " NAG S 614 " - " ASN S 276 " " NAG S 615 " - " ASN S 295 " " NAG S 616 " - " ASN S 301 " " NAG S 617 " - " ASN S 332 " " NAG S 618 " - " ASN S 339 " " NAG S 619 " - " ASN S 355 " " NAG S 620 " - " ASN S 363 " " NAG S 623 " - " ASN S 392 " " NAG T 701 " - " ASN T 611 " " NAG T 702 " - " ASN T 618 " " NAG T 703 " - " ASN T 625 " " NAG T 704 " - " ASN T 637 " " NAG W 1 " - " ASN S 156 " " NAG X 1 " - " ASN S 197 " " NAG Y 1 " - " ASN S 262 " " NAG Z 1 " - " ASN S 386 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 890.6 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 45 sheets defined 21.4% alpha, 37.4% 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 115 removed outlier: 4.195A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.015A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.763A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.437A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.542A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 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 660 removed outlier: 3.602A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 4.015A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.763A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 removed outlier: 4.438A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.542A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 removed outlier: 3.602A pdb=" N GLN J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'S' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU S 102 " --> pdb=" O ASN S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 126 Processing helix chain 'S' and resid 139 through 151 Processing helix chain 'S' and resid 195 through 198 Processing helix chain 'S' and resid 334 through 354 removed outlier: 4.015A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS S 352 " --> pdb=" O GLN S 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 368 through 373 Processing helix chain 'S' and resid 476 through 484 removed outlier: 3.764A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 528 removed outlier: 4.437A pdb=" N GLY T 527 " --> pdb=" O GLY T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 removed outlier: 3.542A pdb=" N GLN T 540 " --> pdb=" O THR T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 596 Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 660 removed outlier: 3.603A pdb=" N GLN T 658 " --> pdb=" O GLU T 654 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 Processing sheet with id=1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.776A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.540A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.657A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.179A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 271 through 274 removed outlier: 12.179A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.555A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=11, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.031A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=13, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=16, first strand: chain 'I' and resid 494 through 498 Processing sheet with id=17, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.776A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=19, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=20, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=21, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.540A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'I' and resid 259 through 261 removed outlier: 3.657A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.179A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'I' and resid 271 through 274 removed outlier: 12.179A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.555A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'K' and resid 3 through 8 Processing sheet with id=26, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.032A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=28, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.643A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.643A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=31, first strand: chain 'S' and resid 494 through 498 Processing sheet with id=32, first strand: chain 'S' and resid 45 through 47 removed outlier: 3.776A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL S 242 " --> pdb=" O LEU S 86 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'S' and resid 75 through 76 Processing sheet with id=34, first strand: chain 'S' and resid 91 through 94 Processing sheet with id=35, first strand: chain 'S' and resid 169 through 177 Processing sheet with id=36, first strand: chain 'S' and resid 201 through 203 removed outlier: 6.540A pdb=" N THR S 202 " --> pdb=" O TYR S 435 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'S' and resid 259 through 261 removed outlier: 3.658A pdb=" N GLY S 451 " --> pdb=" O LEU S 260 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 12.178A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE S 382 " --> pdb=" O LYS S 421 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'S' and resid 271 through 274 removed outlier: 12.178A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'S' and resid 304 through 312 removed outlier: 6.555A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'U' and resid 3 through 8 Processing sheet with id=41, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.031A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'U' and resid 11 through 12 Processing sheet with id=43, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP V 35 " --> pdb=" O MET V 47 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'V' and resid 19 through 24 789 hydrogen bonds defined for protein. 2025 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: 4.15 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3525 1.31 - 1.44: 5410 1.44 - 1.57: 10801 1.57 - 1.69: 64 1.69 - 1.82: 174 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG B 703 " pdb=" O5 NAG B 703 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG T 703 " pdb=" O5 NAG T 703 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG J 703 " pdb=" O5 NAG J 703 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.88e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 23225 2.34 - 4.67: 3343 4.67 - 7.01: 456 7.01 - 9.35: 57 9.35 - 11.68: 12 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 122.38 -11.68 1.22e+00 6.72e-01 9.17e+01 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 122.38 -11.68 1.22e+00 6.72e-01 9.16e+01 angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 122.38 -11.68 1.22e+00 6.72e-01 9.16e+01 angle pdb=" C GLU S 492 " pdb=" N PRO S 493 " pdb=" CA PRO S 493 " ideal model delta sigma weight residual 119.56 127.33 -7.77 1.01e+00 9.80e-01 5.92e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.30 -7.74 1.01e+00 9.80e-01 5.87e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 10770 16.72 - 33.45: 300 33.45 - 50.17: 102 50.17 - 66.89: 33 66.89 - 83.62: 18 Dihedral angle restraints: 11223 sinusoidal: 4476 harmonic: 6747 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.30 -70.30 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS S 228 " pdb=" SG CYS S 228 " pdb=" SG CYS S 239 " pdb=" CB CYS S 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.30 -70.30 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.27 -70.27 1 1.00e+01 1.00e-02 6.36e+01 ... (remaining 11220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2249 0.093 - 0.185: 796 0.185 - 0.278: 204 0.278 - 0.370: 27 0.370 - 0.463: 3 Chirality restraints: 3279 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.50e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.057 2.00e-02 2.50e+03 4.71e-02 2.77e+01 pdb=" C7 NAG B 702 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.057 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" C7 NAG T 702 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.057 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" C7 NAG J 702 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.012 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 6654 2.84 - 3.36: 16547 3.36 - 3.87: 32269 3.87 - 4.39: 37908 4.39 - 4.90: 63051 Nonbonded interactions: 156429 Sorted by model distance: nonbonded pdb=" N ASN I 355 " pdb=" OD1 ASN I 355 " model vdw 2.329 3.120 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.329 3.120 nonbonded pdb=" N ASN S 355 " pdb=" OD1 ASN S 355 " model vdw 2.330 3.120 nonbonded pdb=" N LEU K 100A" pdb=" N GLN K 100B" model vdw 2.331 2.560 nonbonded pdb=" N LEU H 100A" pdb=" N GLN H 100B" model vdw 2.332 2.560 ... (remaining 156424 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: 0.06 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'V' } 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: 1.420 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.950 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.025 0.145 20097 Z= 1.285 Angle : 1.723 11.683 27426 Z= 1.112 Chirality : 0.099 0.463 3279 Planarity : 0.009 0.061 3339 Dihedral : 10.143 83.617 6783 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.65 % Favored : 96.09 % Rotamer: Outliers : 0.44 % Allowed : 0.15 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2304 helix: -0.30 (0.25), residues: 387 sheet: 0.81 (0.20), residues: 666 loop : 0.48 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 53 TYR 0.054 0.008 TYR L 36 PHE 0.036 0.006 PHE I 383 TRP 0.065 0.011 TRP S 479 HIS 0.006 0.002 HIS H 82A Details of bonding type rmsd/Z covalent geometry : bond 0.02479 / 1.28 (19974) covalent geometry : angle 1.69511 / 1.11 (27093) SS BOND : bond 0.04003 / 2.81 ( 36) SS BOND : angle 2.75150 / 1.90 ( 72) hydrogen bonds : bond 0.16341 / 11.31 ( 744) hydrogen bonds : angle 7.00542 / 4.95 ( 2025) link_ALPHA1-3 : bond 0.03405 / 1.71 ( 3) link_ALPHA1-3 : angle 2.80175 / 1.87 ( 9) link_BETA1-4 : bond 0.02706 / 1.50 ( 18) link_BETA1-4 : angle 3.80411 / 2.69 ( 54) link_NAG-ASN : bond 0.03269 / 1.99 ( 66) link_NAG-ASN : angle 3.29133 / 2.35 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 444 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7835 (mtp) cc_final: 0.7634 (mtp) REVERT: H 82 MET cc_start: 0.8617 (mtt) cc_final: 0.8401 (mtt) REVERT: L 94 ARG cc_start: 0.5628 (mmt180) cc_final: 0.4648 (mtm-85) REVERT: I 277 ILE cc_start: 0.8783 (tp) cc_final: 0.8521 (tp) REVERT: M 94 ARG cc_start: 0.5849 (mmt180) cc_final: 0.4832 (mtm-85) REVERT: V 94 ARG cc_start: 0.5814 (mmt180) cc_final: 0.4800 (mtm-85) outliers start: 9 outliers final: 4 residues processed: 447 average time/residue: 0.1709 time to fit residues: 111.0694 Evaluate side-chains 265 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 261 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain T residue 618 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 39 HIS I 103 GLN I 246 GLN I 302 ASN ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN M 39 HIS ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.103424 restraints weight = 25197.974| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.61 r_work: 0.2891 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20097 Z= 0.172 Angle : 0.728 8.736 27426 Z= 0.377 Chirality : 0.046 0.195 3279 Planarity : 0.004 0.037 3339 Dihedral : 5.375 30.913 2528 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.21 % Favored : 96.53 % Rotamer: Outliers : 1.91 % Allowed : 4.79 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2304 helix: 1.50 (0.28), residues: 384 sheet: 0.51 (0.19), residues: 687 loop : 0.15 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 71 TYR 0.014 0.001 TYR M 96 PHE 0.021 0.002 PHE S 383 TRP 0.018 0.001 TRP S 479 HIS 0.005 0.001 HIS U 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (19974) covalent geometry : angle 0.68564 / 0.37 (27093) SS BOND : bond 0.00377 / 0.25 ( 36) SS BOND : angle 0.99669 / 0.71 ( 72) hydrogen bonds : bond 0.05914 / 4.02 ( 744) hydrogen bonds : angle 5.62074 / 3.93 ( 2025) link_ALPHA1-3 : bond 0.00515 / 0.26 ( 3) link_ALPHA1-3 : angle 1.38410 / 0.84 ( 9) link_BETA1-4 : bond 0.00516 / 0.30 ( 18) link_BETA1-4 : angle 2.19365 / 1.58 ( 54) link_NAG-ASN : bond 0.00332 / 0.20 ( 66) link_NAG-ASN : angle 2.71943 / 1.94 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 299 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8047 (mt0) cc_final: 0.7522 (tt0) REVERT: A 232 LYS cc_start: 0.8159 (mttt) cc_final: 0.7910 (ptpt) REVERT: H 23 ARG cc_start: 0.8397 (tpt170) cc_final: 0.8192 (ttm-80) REVERT: H 75 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8240 (mttp) REVERT: L 54 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.8072 (mtp-110) REVERT: L 94 ARG cc_start: 0.6152 (mmt180) cc_final: 0.3742 (mtm-85) REVERT: I 375 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8964 (p) REVERT: K 75 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8282 (mtpt) REVERT: M 54 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8190 (mtp-110) REVERT: M 94 ARG cc_start: 0.6032 (mmt180) cc_final: 0.3708 (mtm-85) REVERT: V 54 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8149 (mtp-110) REVERT: V 94 ARG cc_start: 0.6242 (mmt180) cc_final: 0.3788 (mtm-85) outliers start: 39 outliers final: 27 residues processed: 324 average time/residue: 0.1572 time to fit residues: 76.8786 Evaluate side-chains 270 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS ** H 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 GLN S 374 HIS S 377 ASN T 652 GLN V 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.102016 restraints weight = 24840.700| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.44 r_work: 0.2864 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20097 Z= 0.200 Angle : 0.675 8.844 27426 Z= 0.340 Chirality : 0.046 0.214 3279 Planarity : 0.005 0.053 3339 Dihedral : 5.306 33.613 2528 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.65 % Favored : 96.09 % Rotamer: Outliers : 2.44 % Allowed : 6.79 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2304 helix: 1.50 (0.27), residues: 381 sheet: 0.39 (0.19), residues: 708 loop : -0.08 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 71 TYR 0.018 0.002 TYR V 49 PHE 0.022 0.002 PHE I 383 TRP 0.012 0.002 TRP K 103 HIS 0.005 0.002 HIS K 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (19974) covalent geometry : angle 0.64008 / 0.33 (27093) SS BOND : bond 0.00378 / 0.26 ( 36) SS BOND : angle 1.00057 / 0.70 ( 72) hydrogen bonds : bond 0.05246 / 3.55 ( 744) hydrogen bonds : angle 5.09962 / 3.55 ( 2025) link_ALPHA1-3 : bond 0.00503 / 0.25 ( 3) link_ALPHA1-3 : angle 1.40974 / 0.89 ( 9) link_BETA1-4 : bond 0.00542 / 0.31 ( 18) link_BETA1-4 : angle 1.42430 / 0.99 ( 54) link_NAG-ASN : bond 0.00437 / 0.22 ( 66) link_NAG-ASN : angle 2.44014 / 1.72 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8060 (mt0) cc_final: 0.7551 (tt0) REVERT: A 136 ASN cc_start: 0.7778 (m-40) cc_final: 0.7553 (m-40) REVERT: A 232 LYS cc_start: 0.8322 (mttt) cc_final: 0.7761 (ptpp) REVERT: H 23 ARG cc_start: 0.8362 (tpt170) cc_final: 0.8152 (ttm-80) REVERT: L 49 TYR cc_start: 0.9298 (p90) cc_final: 0.8717 (p90) REVERT: L 54 ARG cc_start: 0.8620 (mtm-85) cc_final: 0.8020 (mtp-110) REVERT: L 94 ARG cc_start: 0.5996 (mmt180) cc_final: 0.3494 (mtm-85) REVERT: I 232 LYS cc_start: 0.8219 (mttp) cc_final: 0.7994 (ptpt) REVERT: J 636 SER cc_start: 0.9095 (t) cc_final: 0.8870 (p) REVERT: K 82 LEU cc_start: 0.7091 (mt) cc_final: 0.6847 (mt) REVERT: M 53 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8737 (mm-40) REVERT: M 54 ARG cc_start: 0.8669 (mtm-85) cc_final: 0.8281 (mtp-110) REVERT: M 94 ARG cc_start: 0.5938 (mmt180) cc_final: 0.3480 (mtm-85) REVERT: U 30 SER cc_start: 0.9191 (OUTLIER) cc_final: 0.8972 (m) REVERT: V 47 MET cc_start: 0.9088 (mmm) cc_final: 0.8689 (mmm) REVERT: V 54 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8195 (mtp-110) REVERT: V 86 TYR cc_start: 0.8356 (m-80) cc_final: 0.8005 (m-10) REVERT: V 94 ARG cc_start: 0.6226 (mmt180) cc_final: 0.3810 (mtm-85) outliers start: 50 outliers final: 37 residues processed: 300 average time/residue: 0.1568 time to fit residues: 69.8097 Evaluate side-chains 283 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 159 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 2 optimal weight: 0.0000 chunk 145 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 82AHIS L 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098039 restraints weight = 25071.238| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.69 r_work: 0.2820 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20097 Z= 0.167 Angle : 0.603 7.452 27426 Z= 0.305 Chirality : 0.045 0.214 3279 Planarity : 0.004 0.055 3339 Dihedral : 4.986 33.067 2522 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.91 % Favored : 95.96 % Rotamer: Outliers : 2.54 % Allowed : 7.97 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.17), residues: 2304 helix: 1.65 (0.27), residues: 381 sheet: 0.34 (0.19), residues: 705 loop : -0.19 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 444 TYR 0.015 0.001 TYR V 49 PHE 0.018 0.002 PHE S 383 TRP 0.010 0.001 TRP A 479 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (19974) covalent geometry : angle 0.57319 / 0.30 (27093) SS BOND : bond 0.00357 / 0.24 ( 36) SS BOND : angle 0.77867 / 0.54 ( 72) hydrogen bonds : bond 0.04778 / 3.23 ( 744) hydrogen bonds : angle 4.90331 / 3.41 ( 2025) link_ALPHA1-3 : bond 0.00280 / 0.14 ( 3) link_ALPHA1-3 : angle 1.41963 / 0.89 ( 9) link_BETA1-4 : bond 0.00438 / 0.26 ( 18) link_BETA1-4 : angle 1.40539 / 0.97 ( 54) link_NAG-ASN : bond 0.00237 / 0.13 ( 66) link_NAG-ASN : angle 2.14482 / 1.52 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.7954 (mt0) cc_final: 0.7631 (tt0) REVERT: A 213 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8068 (mm) REVERT: A 232 LYS cc_start: 0.8239 (mttt) cc_final: 0.7705 (ptpp) REVERT: A 444 ARG cc_start: 0.8271 (ttt90) cc_final: 0.8068 (ttt-90) REVERT: B 636 SER cc_start: 0.8988 (t) cc_final: 0.8736 (p) REVERT: H 23 ARG cc_start: 0.8297 (tpt170) cc_final: 0.8095 (ttm-80) REVERT: H 82 MET cc_start: 0.8711 (mtm) cc_final: 0.8313 (mtt) REVERT: L 49 TYR cc_start: 0.9268 (p90) cc_final: 0.8755 (p90) REVERT: L 54 ARG cc_start: 0.8562 (mtm-85) cc_final: 0.8004 (mtp-110) REVERT: L 94 ARG cc_start: 0.5692 (mmt180) cc_final: 0.3604 (mtm-85) REVERT: M 53 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8706 (mm-40) REVERT: M 54 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.7966 (mtp-110) REVERT: M 94 ARG cc_start: 0.5658 (mmt180) cc_final: 0.3507 (mtm-85) REVERT: T 636 SER cc_start: 0.8861 (t) cc_final: 0.8631 (p) REVERT: U 30 SER cc_start: 0.9098 (OUTLIER) cc_final: 0.8880 (m) REVERT: V 54 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8120 (mtp-110) REVERT: V 94 ARG cc_start: 0.6042 (mmt180) cc_final: 0.3814 (mtm-85) outliers start: 52 outliers final: 34 residues processed: 292 average time/residue: 0.1729 time to fit residues: 74.0249 Evaluate side-chains 275 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 135 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 180 optimal weight: 0.2980 chunk 228 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.095318 restraints weight = 25183.597| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.64 r_work: 0.2868 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 20097 Z= 0.331 Angle : 0.760 13.951 27426 Z= 0.377 Chirality : 0.050 0.284 3279 Planarity : 0.005 0.058 3339 Dihedral : 5.385 32.588 2522 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.43 % Favored : 95.44 % Rotamer: Outliers : 3.32 % Allowed : 7.38 % Favored : 89.30 % 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 are not related in a simple way. whole: -0.09 (0.17), residues: 2304 helix: 1.08 (0.26), residues: 384 sheet: 0.15 (0.20), residues: 654 loop : -0.49 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 444 TYR 0.017 0.002 TYR V 49 PHE 0.022 0.003 PHE I 383 TRP 0.014 0.002 TRP A 427 HIS 0.007 0.001 HIS K 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.33 (19974) covalent geometry : angle 0.72415 / 0.37 (27093) SS BOND : bond 0.00572 / 0.39 ( 36) SS BOND : angle 1.24939 / 0.87 ( 72) hydrogen bonds : bond 0.06125 / 4.16 ( 744) hydrogen bonds : angle 5.10712 / 3.57 ( 2025) link_ALPHA1-3 : bond 0.00265 / 0.13 ( 3) link_ALPHA1-3 : angle 1.71497 / 1.10 ( 9) link_BETA1-4 : bond 0.00507 / 0.31 ( 18) link_BETA1-4 : angle 1.56035 / 1.06 ( 54) link_NAG-ASN : bond 0.00493 / 0.28 ( 66) link_NAG-ASN : angle 2.64418 / 1.83 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 244 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8089 (mt0) cc_final: 0.7728 (tt0) REVERT: A 151 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7854 (ttm170) REVERT: A 444 ARG cc_start: 0.8498 (ttt90) cc_final: 0.8291 (ttt180) REVERT: B 636 SER cc_start: 0.9053 (t) cc_final: 0.8808 (p) REVERT: L 17 GLN cc_start: 0.6749 (mt0) cc_final: 0.6514 (tp-100) REVERT: L 54 ARG cc_start: 0.8651 (mtm-85) cc_final: 0.8429 (mtm110) REVERT: L 94 ARG cc_start: 0.6383 (mmt180) cc_final: 0.3792 (mtm-85) REVERT: M 42 LYS cc_start: 0.8445 (mmmm) cc_final: 0.7348 (mtmm) REVERT: M 53 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8832 (mm-40) REVERT: M 54 ARG cc_start: 0.8689 (mtm-85) cc_final: 0.8310 (mtp-110) REVERT: M 94 ARG cc_start: 0.6290 (mmt180) cc_final: 0.3622 (mtm-85) REVERT: U 30 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.9000 (m) REVERT: V 42 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8452 (mmmm) REVERT: V 54 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.8196 (mtp-110) REVERT: V 86 TYR cc_start: 0.8579 (m-80) cc_final: 0.8333 (m-10) REVERT: V 94 ARG cc_start: 0.6408 (mmt180) cc_final: 0.3813 (mtm-85) outliers start: 68 outliers final: 51 residues processed: 288 average time/residue: 0.1684 time to fit residues: 71.6071 Evaluate side-chains 290 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 455 THR Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 38 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099511 restraints weight = 24977.667| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.76 r_work: 0.2862 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20097 Z= 0.124 Angle : 0.598 11.373 27426 Z= 0.295 Chirality : 0.044 0.336 3279 Planarity : 0.004 0.056 3339 Dihedral : 4.949 26.102 2522 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.65 % Favored : 96.22 % Rotamer: Outliers : 1.91 % Allowed : 9.19 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.18), residues: 2304 helix: 1.76 (0.28), residues: 381 sheet: 0.17 (0.19), residues: 726 loop : -0.40 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 178 TYR 0.017 0.001 TYR M 49 PHE 0.014 0.001 PHE I 383 TRP 0.010 0.001 TRP A 479 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (19974) covalent geometry : angle 0.56193 / 0.29 (27093) SS BOND : bond 0.00265 / 0.18 ( 36) SS BOND : angle 0.69347 / 0.50 ( 72) hydrogen bonds : bond 0.04366 / 2.93 ( 744) hydrogen bonds : angle 4.80936 / 3.35 ( 2025) link_ALPHA1-3 : bond 0.00341 / 0.17 ( 3) link_ALPHA1-3 : angle 1.48923 / 0.94 ( 9) link_BETA1-4 : bond 0.00442 / 0.26 ( 18) link_BETA1-4 : angle 1.39794 / 0.96 ( 54) link_NAG-ASN : bond 0.00227 / 0.12 ( 66) link_NAG-ASN : angle 2.35835 / 1.61 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8046 (mt0) cc_final: 0.7718 (tt0) REVERT: A 213 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8213 (mm) REVERT: B 635 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8411 (tt) REVERT: H 100 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8864 (mp) REVERT: L 17 GLN cc_start: 0.6782 (mt0) cc_final: 0.6538 (tp-100) REVERT: L 49 TYR cc_start: 0.9338 (p90) cc_final: 0.8844 (p90) REVERT: L 94 ARG cc_start: 0.6098 (mmt180) cc_final: 0.3617 (mtm-85) REVERT: I 114 GLN cc_start: 0.8001 (mt0) cc_final: 0.7533 (tt0) REVERT: I 213 ILE cc_start: 0.8321 (tt) cc_final: 0.8040 (mm) REVERT: K 100 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9043 (mp) REVERT: M 42 LYS cc_start: 0.8519 (mmmm) cc_final: 0.7379 (mtmm) REVERT: M 53 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8828 (mm-40) REVERT: M 54 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8017 (mtp-110) REVERT: M 94 ARG cc_start: 0.6053 (mmt180) cc_final: 0.3524 (mtm-85) REVERT: S 381 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: S 475 MET cc_start: 0.8977 (tpp) cc_final: 0.8734 (tpp) REVERT: U 30 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8972 (m) REVERT: U 43 LYS cc_start: 0.7565 (mppt) cc_final: 0.7235 (mmmm) REVERT: V 42 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8375 (mmmm) REVERT: V 47 MET cc_start: 0.9076 (mmm) cc_final: 0.8722 (mmm) REVERT: V 54 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.7934 (mtp-110) REVERT: V 85 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8247 (t0) REVERT: V 86 TYR cc_start: 0.8372 (m-80) cc_final: 0.8081 (m-10) REVERT: V 94 ARG cc_start: 0.6401 (mmt180) cc_final: 0.3759 (mtm-85) outliers start: 39 outliers final: 25 residues processed: 274 average time/residue: 0.1742 time to fit residues: 69.1852 Evaluate side-chains 268 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 381 GLU Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.098552 restraints weight = 25132.468| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.63 r_work: 0.2805 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20097 Z= 0.148 Angle : 0.591 8.698 27426 Z= 0.293 Chirality : 0.044 0.220 3279 Planarity : 0.004 0.057 3339 Dihedral : 4.816 26.618 2520 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.47 % Favored : 95.40 % Rotamer: Outliers : 2.59 % Allowed : 9.09 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 2304 helix: 1.84 (0.28), residues: 381 sheet: 0.19 (0.19), residues: 714 loop : -0.34 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 178 TYR 0.016 0.001 TYR V 49 PHE 0.016 0.002 PHE I 383 TRP 0.010 0.001 TRP A 479 HIS 0.003 0.001 HIS U 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (19974) covalent geometry : angle 0.56043 / 0.29 (27093) SS BOND : bond 0.00310 / 0.21 ( 36) SS BOND : angle 0.82519 / 0.58 ( 72) hydrogen bonds : bond 0.04514 / 3.05 ( 744) hydrogen bonds : angle 4.72849 / 3.30 ( 2025) link_ALPHA1-3 : bond 0.00329 / 0.16 ( 3) link_ALPHA1-3 : angle 1.58515 / 1.01 ( 9) link_BETA1-4 : bond 0.00451 / 0.27 ( 18) link_BETA1-4 : angle 1.38379 / 0.95 ( 54) link_NAG-ASN : bond 0.00228 / 0.13 ( 66) link_NAG-ASN : angle 2.12683 / 1.48 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8156 (mttm) REVERT: A 114 GLN cc_start: 0.7924 (mt0) cc_final: 0.7668 (tt0) REVERT: A 213 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8257 (mm) REVERT: B 636 SER cc_start: 0.8964 (p) cc_final: 0.8762 (p) REVERT: H 100 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8828 (mp) REVERT: L 49 TYR cc_start: 0.9246 (p90) cc_final: 0.8811 (p90) REVERT: L 94 ARG cc_start: 0.5708 (mmt180) cc_final: 0.3651 (mtm-85) REVERT: I 114 GLN cc_start: 0.7918 (mt0) cc_final: 0.7497 (tt0) REVERT: I 213 ILE cc_start: 0.8239 (tt) cc_final: 0.8007 (mm) REVERT: K 100 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9005 (mp) REVERT: M 42 LYS cc_start: 0.8455 (mmmm) cc_final: 0.7472 (mtmm) REVERT: M 53 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8783 (mm-40) REVERT: M 54 ARG cc_start: 0.8655 (mtm-85) cc_final: 0.8031 (mtp-110) REVERT: M 94 ARG cc_start: 0.5606 (mmt180) cc_final: 0.3443 (mtm-85) REVERT: S 381 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: T 626 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8622 (mtp) REVERT: U 30 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8888 (m) REVERT: U 43 LYS cc_start: 0.7542 (mppt) cc_final: 0.7097 (mmmm) REVERT: U 100 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9094 (mp) REVERT: V 42 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8362 (mmmm) REVERT: V 47 MET cc_start: 0.8988 (mmm) cc_final: 0.8606 (mmm) REVERT: V 54 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8132 (mtp-110) REVERT: V 85 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8231 (t0) REVERT: V 86 TYR cc_start: 0.8336 (m-80) cc_final: 0.8073 (m-10) REVERT: V 94 ARG cc_start: 0.6094 (mmt180) cc_final: 0.3775 (mtm-85) outliers start: 53 outliers final: 37 residues processed: 280 average time/residue: 0.1566 time to fit residues: 64.6204 Evaluate side-chains 289 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 381 GLU Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 188 optimal weight: 0.9980 chunk 13 optimal weight: 0.0070 chunk 173 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 205 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.100858 restraints weight = 24994.660| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.58 r_work: 0.2836 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20097 Z= 0.109 Angle : 0.554 8.996 27426 Z= 0.276 Chirality : 0.043 0.219 3279 Planarity : 0.004 0.056 3339 Dihedral : 4.670 24.066 2520 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.88 % Rotamer: Outliers : 2.49 % Allowed : 9.19 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2304 helix: 2.08 (0.28), residues: 381 sheet: 0.33 (0.19), residues: 726 loop : -0.30 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 444 TYR 0.015 0.001 TYR V 49 PHE 0.014 0.001 PHE S 383 TRP 0.009 0.001 TRP A 479 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (19974) covalent geometry : angle 0.52630 / 0.27 (27093) SS BOND : bond 0.00226 / 0.15 ( 36) SS BOND : angle 0.61372 / 0.44 ( 72) hydrogen bonds : bond 0.04043 / 2.72 ( 744) hydrogen bonds : angle 4.62463 / 3.22 ( 2025) link_ALPHA1-3 : bond 0.00350 / 0.18 ( 3) link_ALPHA1-3 : angle 1.54922 / 0.98 ( 9) link_BETA1-4 : bond 0.00425 / 0.25 ( 18) link_BETA1-4 : angle 1.35439 / 0.93 ( 54) link_NAG-ASN : bond 0.00186 / 0.12 ( 66) link_NAG-ASN : angle 1.95920 / 1.39 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8127 (mttm) REVERT: A 213 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8184 (mm) REVERT: B 635 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8311 (tt) REVERT: H 100 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8886 (mp) REVERT: L 49 TYR cc_start: 0.9195 (p90) cc_final: 0.8741 (p90) REVERT: L 94 ARG cc_start: 0.5711 (mmt180) cc_final: 0.3712 (mtm-85) REVERT: I 114 GLN cc_start: 0.7871 (mt0) cc_final: 0.7487 (tt0) REVERT: I 213 ILE cc_start: 0.8184 (tt) cc_final: 0.7961 (mm) REVERT: I 381 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7790 (tp30) REVERT: K 100 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9055 (mp) REVERT: M 42 LYS cc_start: 0.8449 (mmmm) cc_final: 0.7462 (mtmm) REVERT: M 53 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8790 (mm-40) REVERT: M 54 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.8065 (mtp-110) REVERT: M 94 ARG cc_start: 0.5642 (mmt180) cc_final: 0.3528 (mtm-85) REVERT: S 381 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7869 (tp30) REVERT: T 626 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8364 (mtp) REVERT: U 30 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8878 (m) REVERT: U 43 LYS cc_start: 0.7557 (mppt) cc_final: 0.7083 (mmmm) REVERT: U 100 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9133 (mt) REVERT: V 42 LYS cc_start: 0.8478 (mmmm) cc_final: 0.8259 (mmmm) REVERT: V 54 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.7940 (mtp-110) REVERT: V 85 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8253 (t0) REVERT: V 86 TYR cc_start: 0.8307 (m-80) cc_final: 0.8020 (m-10) REVERT: V 94 ARG cc_start: 0.5925 (mmt180) cc_final: 0.3753 (mtm-85) outliers start: 51 outliers final: 32 residues processed: 296 average time/residue: 0.1660 time to fit residues: 73.2836 Evaluate side-chains 290 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 381 GLU Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.095424 restraints weight = 24997.420| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.75 r_work: 0.2795 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20097 Z= 0.260 Angle : 0.688 13.950 27426 Z= 0.340 Chirality : 0.048 0.270 3279 Planarity : 0.005 0.056 3339 Dihedral : 5.009 25.205 2520 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 2.69 % Allowed : 9.63 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2304 helix: 1.26 (0.27), residues: 402 sheet: 0.16 (0.19), residues: 711 loop : -0.45 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 444 TYR 0.015 0.002 TYR V 49 PHE 0.019 0.002 PHE I 383 TRP 0.012 0.002 TRP T 631 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.26 (19974) covalent geometry : angle 0.65029 / 0.33 (27093) SS BOND : bond 0.00482 / 0.33 ( 36) SS BOND : angle 1.09570 / 0.77 ( 72) hydrogen bonds : bond 0.05411 / 3.68 ( 744) hydrogen bonds : angle 4.85410 / 3.40 ( 2025) link_ALPHA1-3 : bond 0.00239 / 0.12 ( 3) link_ALPHA1-3 : angle 1.81933 / 1.17 ( 9) link_BETA1-4 : bond 0.00450 / 0.27 ( 18) link_BETA1-4 : angle 1.47008 / 1.00 ( 54) link_NAG-ASN : bond 0.00386 / 0.22 ( 66) link_NAG-ASN : angle 2.56359 / 1.79 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 241 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8297 (mttm) REVERT: A 213 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8378 (mm) REVERT: H 100 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8775 (mp) REVERT: L 49 TYR cc_start: 0.9409 (p90) cc_final: 0.8939 (p90) REVERT: L 94 ARG cc_start: 0.6393 (mmt180) cc_final: 0.3909 (mtm-85) REVERT: I 213 ILE cc_start: 0.8487 (tt) cc_final: 0.8154 (mm) REVERT: I 381 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8065 (tp30) REVERT: I 434 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9134 (ttp) REVERT: M 42 LYS cc_start: 0.8450 (mmmm) cc_final: 0.7366 (mtmm) REVERT: M 53 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8826 (mm-40) REVERT: M 54 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8056 (mtp-110) REVERT: M 94 ARG cc_start: 0.6157 (mmt180) cc_final: 0.3478 (mtm-85) REVERT: S 381 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8169 (tp30) REVERT: U 30 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8908 (m) REVERT: U 43 LYS cc_start: 0.7593 (mppt) cc_final: 0.7171 (mmmm) REVERT: U 100 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8978 (mp) REVERT: V 42 LYS cc_start: 0.8470 (mmmm) cc_final: 0.8233 (mmmm) REVERT: V 54 ARG cc_start: 0.8542 (mtm-85) cc_final: 0.8177 (mtp-110) REVERT: V 85 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8285 (t0) REVERT: V 86 TYR cc_start: 0.8481 (m-80) cc_final: 0.8222 (m-10) REVERT: V 94 ARG cc_start: 0.6385 (mmt180) cc_final: 0.3813 (mtm-85) outliers start: 55 outliers final: 39 residues processed: 277 average time/residue: 0.1632 time to fit residues: 66.9246 Evaluate side-chains 281 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 381 GLU Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 27 ASP Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 226 optimal weight: 0.0270 chunk 91 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 208 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 196 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101809 restraints weight = 25046.570| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.64 r_work: 0.2966 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20097 Z= 0.105 Angle : 0.560 9.640 27426 Z= 0.279 Chirality : 0.043 0.264 3279 Planarity : 0.004 0.056 3339 Dihedral : 4.673 24.457 2520 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 1.61 % Allowed : 10.95 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.18), residues: 2304 helix: 2.05 (0.28), residues: 381 sheet: 0.37 (0.19), residues: 726 loop : -0.37 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 444 TYR 0.015 0.001 TYR V 49 PHE 0.013 0.001 PHE I 383 TRP 0.009 0.001 TRP I 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (19974) covalent geometry : angle 0.52954 / 0.27 (27093) SS BOND : bond 0.00208 / 0.14 ( 36) SS BOND : angle 0.59072 / 0.42 ( 72) hydrogen bonds : bond 0.03952 / 2.65 ( 744) hydrogen bonds : angle 4.65381 / 3.24 ( 2025) link_ALPHA1-3 : bond 0.00319 / 0.16 ( 3) link_ALPHA1-3 : angle 1.53585 / 0.97 ( 9) link_BETA1-4 : bond 0.00411 / 0.24 ( 18) link_BETA1-4 : angle 1.38838 / 0.95 ( 54) link_NAG-ASN : bond 0.00219 / 0.13 ( 66) link_NAG-ASN : angle 2.08316 / 1.46 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8171 (mttm) REVERT: A 213 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8196 (mm) REVERT: A 271 MET cc_start: 0.8750 (mmt) cc_final: 0.8513 (mmm) REVERT: A 444 ARG cc_start: 0.8236 (ttt90) cc_final: 0.8009 (ttt-90) REVERT: H 100 TYR cc_start: 0.8943 (p90) cc_final: 0.8501 (p90) REVERT: L 49 TYR cc_start: 0.9230 (p90) cc_final: 0.8700 (p90) REVERT: L 94 ARG cc_start: 0.5701 (mmt180) cc_final: 0.3762 (mtm-85) REVERT: I 42 VAL cc_start: 0.9116 (t) cc_final: 0.8891 (m) REVERT: I 114 GLN cc_start: 0.7830 (mt0) cc_final: 0.7490 (tt0) REVERT: I 213 ILE cc_start: 0.8243 (tt) cc_final: 0.8000 (mm) REVERT: K 43 LYS cc_start: 0.7216 (mppt) cc_final: 0.6859 (mmmm) REVERT: K 81 GLN cc_start: 0.8117 (tp40) cc_final: 0.7775 (mm110) REVERT: K 100 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9104 (mp) REVERT: M 42 LYS cc_start: 0.8447 (mmmm) cc_final: 0.7392 (mtmm) REVERT: M 53 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8780 (mm-40) REVERT: M 54 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8068 (mtp-110) REVERT: M 94 ARG cc_start: 0.5616 (mmt180) cc_final: 0.3542 (mtm-85) REVERT: S 381 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: U 30 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8794 (m) REVERT: U 43 LYS cc_start: 0.7534 (mppt) cc_final: 0.7093 (mmmm) REVERT: U 78 LEU cc_start: 0.9071 (mt) cc_final: 0.8853 (mt) REVERT: V 42 LYS cc_start: 0.8450 (mmmm) cc_final: 0.8220 (mmmm) REVERT: V 47 MET cc_start: 0.8981 (mmm) cc_final: 0.8621 (mmm) REVERT: V 54 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.7956 (mtp-110) REVERT: V 85 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8251 (t0) REVERT: V 86 TYR cc_start: 0.8327 (m-80) cc_final: 0.8065 (m-10) REVERT: V 94 ARG cc_start: 0.5935 (mmt180) cc_final: 0.3834 (mtm-85) outliers start: 33 outliers final: 23 residues processed: 280 average time/residue: 0.1688 time to fit residues: 70.0497 Evaluate side-chains 281 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 GLU Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 27 ASP Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 27 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 206 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 191 optimal weight: 0.0050 chunk 75 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099523 restraints weight = 25030.182| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.62 r_work: 0.2948 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20097 Z= 0.161 Angle : 0.593 9.708 27426 Z= 0.295 Chirality : 0.045 0.242 3279 Planarity : 0.004 0.056 3339 Dihedral : 4.707 23.700 2520 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 1.96 % Allowed : 10.95 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2304 helix: 1.71 (0.27), residues: 399 sheet: 0.39 (0.19), residues: 693 loop : -0.48 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 444 TYR 0.015 0.001 TYR L 49 PHE 0.016 0.002 PHE I 383 TRP 0.009 0.001 TRP I 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (19974) covalent geometry : angle 0.56307 / 0.29 (27093) SS BOND : bond 0.00317 / 0.22 ( 36) SS BOND : angle 0.79224 / 0.56 ( 72) hydrogen bonds : bond 0.04507 / 3.05 ( 744) hydrogen bonds : angle 4.70198 / 3.28 ( 2025) link_ALPHA1-3 : bond 0.00320 / 0.16 ( 3) link_ALPHA1-3 : angle 1.65136 / 1.05 ( 9) link_BETA1-4 : bond 0.00440 / 0.26 ( 18) link_BETA1-4 : angle 1.37963 / 0.94 ( 54) link_NAG-ASN : bond 0.00203 / 0.12 ( 66) link_NAG-ASN : angle 2.09199 / 1.46 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4563.30 seconds wall clock time: 79 minutes 3.70 seconds (4743.70 seconds total)