Starting phenix.real_space_refine on Sat Sep 12 22:30:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x97_22103/09_2026/6x97_22103.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x97_22103/09_2026/6x97_22103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x97_22103/09_2026/6x97_22103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x97_22103/09_2026/6x97_22103.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x97_22103/09_2026/6x97_22103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x97_22103/09_2026/6x97_22103.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6x97_22103/09_2026/6x97_22103.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x97_22103/09_2026/6x97_22103.cif" } resolution = 3.65 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= 0.001 sd= 0.070 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 129 5.16 5 C 11862 2.51 5 N 3171 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 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: 18873 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3373 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "B" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 938 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "H" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 804 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "C" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3373 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 938 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "E" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "F" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 804 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "G" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3373 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "I" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 938 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "J" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "K" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 804 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 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: "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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.19, per 1000 atoms: 0.22 Number of scatterers: 18873 At special positions: 0 Unit cell: (145.41, 158.51, 115.28, 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 129 16.00 O 3711 8.00 N 3171 7.00 C 11862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.12 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 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=2.06 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.10 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.07 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.12 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.05 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.06 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.10 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.07 Simple disulfide: pdb=" SG CYS E 35A" - pdb=" SG CYS E 50 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.12 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.05 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.06 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.10 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.07 Simple disulfide: pdb=" SG CYS J 35A" - pdb=" SG CYS J 50 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 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 BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 608 " - " ASN A 332 " " NAG A 611 " - " ASN A 234 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 156 " " NAG A 614 " - " ASN A 160 " " NAG A 615 " - " ASN A 392 " " NAG A 616 " - " ASN A 197 " " NAG A 619 " - " ASN A 339 " " NAG A 620 " - " ASN A 133 " " NAG C 608 " - " ASN C 332 " " NAG C 611 " - " ASN C 234 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 156 " " NAG C 614 " - " ASN C 160 " " NAG C 615 " - " ASN C 392 " " NAG C 616 " - " ASN C 197 " " NAG C 619 " - " ASN C 339 " " NAG C 620 " - " ASN C 133 " " NAG G 608 " - " ASN G 332 " " NAG G 611 " - " ASN G 234 " " NAG G 612 " - " ASN G 386 " " NAG G 613 " - " ASN G 156 " " NAG G 614 " - " ASN G 160 " " NAG G 615 " - " ASN G 392 " " NAG G 616 " - " ASN G 197 " " NAG G 619 " - " ASN G 339 " " NAG G 620 " - " ASN G 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 88 " " NAG Q 1 " - " ASN A 363 " " NAG R 1 " - " ASN C 448 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 295 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN G 448 " " NAG X 1 " - " ASN G 262 " " NAG Y 1 " - " ASN G 295 " " NAG Z 1 " - " ASN G 88 " " NAG a 1 " - " ASN G 363 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 757.8 milliseconds 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4260 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 19.3% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.079A 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 335 through 351 removed outlier: 4.008A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.655A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.016A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.613A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.542A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.079A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 351 removed outlier: 4.008A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'C' and resid 481 through 483 No H-bonds generated for 'chain 'C' and resid 481 through 483' Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 541 removed outlier: 3.655A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 removed outlier: 4.016A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 626 removed outlier: 4.613A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 652 removed outlier: 3.542A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.079A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 335 through 351 removed outlier: 4.007A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 480 Processing helix chain 'G' and resid 481 through 483 No H-bonds generated for 'chain 'G' and resid 481 through 483' Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 541 removed outlier: 3.654A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 596 removed outlier: 4.016A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN I 575 " --> pdb=" O TRP I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 615 Processing helix chain 'I' and resid 618 through 626 removed outlier: 4.613A pdb=" N ASP I 624 " --> pdb=" O SER I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 652 removed outlier: 3.542A pdb=" N GLN I 650 " --> pdb=" O LEU I 646 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.314A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.887A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.072A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.617A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.078A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.921A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.518A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 56 " --> pdb=" O PHE H 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.603A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER H 96 " --> pdb=" O GLY H 100E" (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLY H 100E" --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR H 98 " --> pdb=" O GLY H 100C" (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY H 100C" --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.553A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.541A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.314A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.886A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.072A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.618A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 261 Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 274 Processing sheet with id=AC8, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.921A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.517A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG E 56 " --> pdb=" O PHE E 52 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.604A pdb=" N LEU E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER E 96 " --> pdb=" O GLY E 100E" (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY E 100E" --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR E 98 " --> pdb=" O GLY E 100C" (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY E 100C" --> pdb=" O THR E 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.553A pdb=" N VAL F 11 " --> pdb=" O VAL F 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.540A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.314A pdb=" N VAL I 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL G 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR I 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N TYR G 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS I 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'G' and resid 75 through 76 removed outlier: 6.887A pdb=" N CYS G 54 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.072A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 256 through 257 removed outlier: 3.618A pdb=" N SER G 375 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 259 through 261 Processing sheet with id=AE5, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AE6, first strand: chain 'G' and resid 315 through 323A removed outlier: 6.921A pdb=" N ALA G 316 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE G 309 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP G 322 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.518A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG J 56 " --> pdb=" O PHE J 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.603A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER J 96 " --> pdb=" O GLY J 100E" (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY J 100E" --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR J 98 " --> pdb=" O GLY J 100C" (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY J 100C" --> pdb=" O THR J 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AF2, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.553A pdb=" N VAL K 11 " --> pdb=" O VAL K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.540A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3809 1.32 - 1.46: 6249 1.46 - 1.59: 8957 1.59 - 1.73: 80 1.73 - 1.87: 162 Bond restraints: 19257 Sorted by residual: bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.669 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" CB ILE F 2 " pdb=" CG1 ILE F 2 " ideal model delta sigma weight residual 1.530 1.669 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" CB ILE K 2 " pdb=" CG1 ILE K 2 " ideal model delta sigma weight residual 1.530 1.669 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" CB HIS C 85 " pdb=" CG HIS C 85 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.06e+01 bond pdb=" CB HIS A 85 " pdb=" CG HIS A 85 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.06e+01 ... (remaining 19252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 24178 3.18 - 6.37: 1834 6.37 - 9.55: 133 9.55 - 12.73: 9 12.73 - 15.92: 3 Bond angle restraints: 26157 Sorted by residual: angle pdb=" N VAL L 3 " pdb=" CA VAL L 3 " pdb=" C VAL L 3 " ideal model delta sigma weight residual 111.62 118.48 -6.86 7.90e-01 1.60e+00 7.55e+01 angle pdb=" N VAL F 3 " pdb=" CA VAL F 3 " pdb=" C VAL F 3 " ideal model delta sigma weight residual 111.62 118.47 -6.85 7.90e-01 1.60e+00 7.52e+01 angle pdb=" N VAL K 3 " pdb=" CA VAL K 3 " pdb=" C VAL K 3 " ideal model delta sigma weight residual 111.62 118.47 -6.85 7.90e-01 1.60e+00 7.52e+01 angle pdb=" C ARG G 298 " pdb=" N PRO G 299 " pdb=" CA PRO G 299 " ideal model delta sigma weight residual 119.56 127.63 -8.07 1.01e+00 9.80e-01 6.38e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.62 -8.06 1.01e+00 9.80e-01 6.37e+01 ... (remaining 26152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 10538 16.59 - 33.18: 286 33.18 - 49.77: 96 49.77 - 66.36: 54 66.36 - 82.95: 27 Dihedral angle restraints: 11001 sinusoidal: 4368 harmonic: 6633 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 93.00 173.70 -80.70 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS G 228 " pdb=" SG CYS G 228 " pdb=" SG CYS G 239 " pdb=" CB CYS G 239 " ideal model delta sinusoidal sigma weight residual 93.00 173.70 -80.70 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual 93.00 173.69 -80.69 1 1.00e+01 1.00e-02 8.05e+01 ... (remaining 10998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2091 0.105 - 0.210: 694 0.210 - 0.315: 187 0.315 - 0.420: 107 0.420 - 0.525: 47 Chirality restraints: 3126 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 BMA X 3 " pdb=" O4 NAG X 2 " pdb=" C2 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.14e+02 ... (remaining 3123 not shown) Planarity restraints: 3285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 339 " 0.086 2.00e-02 2.50e+03 8.83e-02 9.76e+01 pdb=" CG ASN A 339 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 339 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 339 " -0.135 2.00e-02 2.50e+03 pdb=" C1 NAG A 619 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 339 " -0.086 2.00e-02 2.50e+03 8.83e-02 9.75e+01 pdb=" CG ASN C 339 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN C 339 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 339 " 0.135 2.00e-02 2.50e+03 pdb=" C1 NAG C 619 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 339 " 0.085 2.00e-02 2.50e+03 8.81e-02 9.70e+01 pdb=" CG ASN G 339 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN G 339 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN G 339 " -0.135 2.00e-02 2.50e+03 pdb=" C1 NAG G 619 " 0.107 2.00e-02 2.50e+03 ... (remaining 3282 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 9760 2.98 - 3.46: 16783 3.46 - 3.94: 31799 3.94 - 4.42: 36193 4.42 - 4.90: 56800 Nonbonded interactions: 151335 Sorted by model distance: nonbonded pdb=" N THR C 50 " pdb=" O THR C 50 " model vdw 2.496 2.496 nonbonded pdb=" N THR A 50 " pdb=" O THR A 50 " model vdw 2.496 2.496 nonbonded pdb=" N THR G 50 " pdb=" O THR G 50 " model vdw 2.496 2.496 nonbonded pdb=" N THR C 303 " pdb=" O THR C 303 " model vdw 2.508 2.496 nonbonded pdb=" N THR A 303 " pdb=" O THR A 303 " model vdw 2.508 2.496 ... (remaining 151330 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.010 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.139 19359 Z= 1.168 Angle : 1.792 15.917 26421 Z= 1.162 Chirality : 0.138 0.525 3126 Planarity : 0.009 0.044 3243 Dihedral : 10.619 82.950 6615 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.40 % 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: 0.36 (0.17), residues: 2265 helix: -0.76 (0.25), residues: 342 sheet: 0.52 (0.19), residues: 672 loop : 0.54 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 166 TYR 0.078 0.010 TYR I 638 PHE 0.031 0.007 PHE C 383 TRP 0.064 0.011 TRP I 628 HIS 0.010 0.003 HIS G 72 Details of bonding type rmsd/Z covalent geometry : bond 0.02184 / 1.15 (19257) covalent geometry : angle 1.76796 / 1.16 (26157) SS BOND : bond 0.03461 / 2.10 ( 42) SS BOND : angle 2.86792 / 1.91 ( 84) hydrogen bonds : bond 0.18936 / 12.35 ( 672) hydrogen bonds : angle 8.00896 / 5.56 ( 1800) link_BETA1-4 : bond 0.07608 / 4.31 ( 18) link_BETA1-4 : angle 4.76795 / 3.26 ( 54) link_NAG-ASN : bond 0.08233 / 5.26 ( 42) link_NAG-ASN : angle 2.99682 / 2.08 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 534 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7773 (m-40) REVERT: A 427 TRP cc_start: 0.7051 (m-10) cc_final: 0.6625 (m-10) REVERT: B 586 TYR cc_start: 0.8766 (t80) cc_final: 0.8543 (t80) REVERT: B 627 THR cc_start: 0.8108 (m) cc_final: 0.7760 (p) REVERT: B 628 TRP cc_start: 0.8452 (t-100) cc_final: 0.8011 (t-100) REVERT: B 657 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7789 (mt-10) REVERT: H 45 LEU cc_start: 0.7735 (mt) cc_final: 0.7391 (mt) REVERT: C 133 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7537 (m-40) REVERT: D 607 ASN cc_start: 0.8216 (m-40) cc_final: 0.7964 (m110) REVERT: D 627 THR cc_start: 0.7876 (m) cc_final: 0.7384 (p) REVERT: D 628 TRP cc_start: 0.8389 (t-100) cc_final: 0.8145 (t-100) REVERT: D 657 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7489 (mt-10) REVERT: E 45 LEU cc_start: 0.7359 (mt) cc_final: 0.6857 (mt) REVERT: E 84 VAL cc_start: 0.8679 (m) cc_final: 0.8460 (t) REVERT: G 150 MET cc_start: 0.7754 (mmm) cc_final: 0.7322 (mmm) REVERT: G 173 TYR cc_start: 0.8079 (p90) cc_final: 0.7798 (p90) REVERT: G 271 MET cc_start: 0.7796 (mmm) cc_final: 0.7570 (mmm) REVERT: G 427 TRP cc_start: 0.7025 (m-10) cc_final: 0.6654 (m-10) outliers start: 6 outliers final: 1 residues processed: 540 average time/residue: 0.1487 time to fit residues: 120.4034 Evaluate side-chains 298 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 295 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain G residue 133 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN B 577 GLN B 591 GLN L 6 GLN C 195 ASN C 249 HIS C 258 GLN C 425 ASN D 630 GLN F 6 GLN G 130 GLN G 195 ASN G 249 HIS G 425 ASN ** I 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 607 ASN K 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.143296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121939 restraints weight = 31581.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.125131 restraints weight = 18959.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.127280 restraints weight = 13363.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.128739 restraints weight = 10408.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.129654 restraints weight = 8679.952| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19359 Z= 0.194 Angle : 0.771 9.218 26421 Z= 0.406 Chirality : 0.049 0.243 3126 Planarity : 0.004 0.036 3243 Dihedral : 5.440 25.455 2475 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.40 % Allowed : 8.26 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2265 helix: 0.56 (0.28), residues: 348 sheet: 0.29 (0.18), residues: 777 loop : 0.05 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 43 TYR 0.019 0.002 TYR D 643 PHE 0.024 0.002 PHE J 52 TRP 0.015 0.002 TRP G 479 HIS 0.005 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (19257) covalent geometry : angle 0.73152 / 0.40 (26157) SS BOND : bond 0.00279 / 0.17 ( 42) SS BOND : angle 1.10304 / 0.74 ( 84) hydrogen bonds : bond 0.06732 / 4.54 ( 672) hydrogen bonds : angle 6.39404 / 4.46 ( 1800) link_BETA1-4 : bond 0.00605 / 0.36 ( 18) link_BETA1-4 : angle 2.85440 / 1.96 ( 54) link_NAG-ASN : bond 0.00492 / 0.32 ( 42) link_NAG-ASN : angle 3.02532 / 2.07 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 377 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.6004 (mpp) cc_final: 0.5761 (mpp) REVERT: C 39 TYR cc_start: 0.8177 (m-80) cc_final: 0.7938 (m-10) REVERT: C 271 MET cc_start: 0.7032 (mmm) cc_final: 0.6826 (mmp) REVERT: C 318 TYR cc_start: 0.7731 (m-80) cc_final: 0.7475 (m-80) REVERT: D 579 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7308 (mtm180) REVERT: D 588 ARG cc_start: 0.8202 (tpt-90) cc_final: 0.7972 (tpp80) REVERT: D 617 ARG cc_start: 0.7149 (mtp-110) cc_final: 0.6749 (mtp-110) REVERT: D 630 GLN cc_start: 0.8249 (mt0) cc_final: 0.7928 (mt0) REVERT: D 648 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8233 (pt0) REVERT: D 651 ASN cc_start: 0.6213 (p0) cc_final: 0.5947 (p0) REVERT: E 45 LEU cc_start: 0.7379 (mt) cc_final: 0.6920 (mt) REVERT: G 150 MET cc_start: 0.7368 (mmm) cc_final: 0.7090 (mmm) REVERT: G 161 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6101 (ttm) REVERT: G 173 TYR cc_start: 0.7807 (p90) cc_final: 0.7606 (p90) REVERT: I 577 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6812 (tt0) REVERT: I 607 ASN cc_start: 0.8211 (m-40) cc_final: 0.7979 (m110) REVERT: I 610 TRP cc_start: 0.8139 (t-100) cc_final: 0.7789 (t-100) REVERT: I 617 ARG cc_start: 0.7494 (mtp-110) cc_final: 0.7166 (mtp-110) REVERT: I 625 ASN cc_start: 0.8752 (m-40) cc_final: 0.8084 (t0) REVERT: I 648 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8480 (mm-30) REVERT: I 650 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7723 (tt0) outliers start: 48 outliers final: 27 residues processed: 403 average time/residue: 0.1341 time to fit residues: 82.4424 Evaluate side-chains 338 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 308 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain I residue 577 GLN Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 212 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 57 optimal weight: 0.0980 chunk 117 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN L 24 GLN C 103 GLN C 130 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN D 607 ASN G 103 GLN G 195 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102294 restraints weight = 32674.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105071 restraints weight = 20606.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106961 restraints weight = 14856.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108243 restraints weight = 11814.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.109105 restraints weight = 10001.688| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19359 Z= 0.144 Angle : 0.650 8.628 26421 Z= 0.338 Chirality : 0.045 0.169 3126 Planarity : 0.004 0.040 3243 Dihedral : 5.086 26.395 2473 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.75 % Allowed : 9.96 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2265 helix: 0.49 (0.28), residues: 357 sheet: 0.30 (0.18), residues: 795 loop : -0.04 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 298 TYR 0.021 0.002 TYR H 90 PHE 0.016 0.002 PHE J 52 TRP 0.018 0.002 TRP D 628 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19257) covalent geometry : angle 0.62509 / 0.33 (26157) SS BOND : bond 0.00193 / 0.13 ( 42) SS BOND : angle 0.89134 / 0.62 ( 84) hydrogen bonds : bond 0.05051 / 3.41 ( 672) hydrogen bonds : angle 5.95121 / 4.14 ( 1800) link_BETA1-4 : bond 0.00663 / 0.39 ( 18) link_BETA1-4 : angle 1.87509 / 1.30 ( 54) link_NAG-ASN : bond 0.00331 / 0.22 ( 42) link_NAG-ASN : angle 2.35991 / 1.62 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7409 (mmm) cc_final: 0.7110 (mmt) REVERT: B 545 LEU cc_start: 0.8292 (mt) cc_final: 0.7970 (mt) REVERT: B 626 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7241 (mtt) REVERT: B 648 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8202 (pt0) REVERT: B 650 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: C 39 TYR cc_start: 0.8292 (m-80) cc_final: 0.7880 (m-10) REVERT: C 271 MET cc_start: 0.7197 (mmm) cc_final: 0.6975 (mmp) REVERT: C 318 TYR cc_start: 0.7845 (m-80) cc_final: 0.7606 (m-80) REVERT: D 579 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7181 (mtm180) REVERT: D 617 ARG cc_start: 0.7118 (mtp-110) cc_final: 0.6689 (mtp-110) REVERT: D 634 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8605 (mm-30) REVERT: D 648 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8255 (pt0) REVERT: D 650 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: F 91 THR cc_start: 0.8503 (p) cc_final: 0.8094 (p) REVERT: G 161 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6224 (ttt) REVERT: I 542 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7594 (ttm170) REVERT: I 577 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6744 (tt0) REVERT: I 610 TRP cc_start: 0.8279 (t-100) cc_final: 0.7851 (t-100) REVERT: I 617 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.7268 (mtp-110) REVERT: I 625 ASN cc_start: 0.8796 (m-40) cc_final: 0.7936 (t0) REVERT: I 648 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8145 (pt0) REVERT: I 649 SER cc_start: 0.9160 (m) cc_final: 0.8905 (t) REVERT: I 650 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: I 651 ASN cc_start: 0.6291 (p0) cc_final: 0.5824 (p0) REVERT: K 69 THR cc_start: 0.8717 (p) cc_final: 0.8397 (p) outliers start: 55 outliers final: 34 residues processed: 378 average time/residue: 0.1473 time to fit residues: 84.3250 Evaluate side-chains 348 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 577 GLN Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 194 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 189 optimal weight: 0.0070 chunk 190 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 chunk 78 optimal weight: 0.0010 chunk 44 optimal weight: 0.0670 chunk 160 optimal weight: 2.9990 overall best weight: 0.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 591 GLN L 24 GLN L 27 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 195 ASN I 591 GLN K 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.102417 restraints weight = 32580.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104867 restraints weight = 21412.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.106574 restraints weight = 15917.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107732 restraints weight = 12857.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108432 restraints weight = 11075.926| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19359 Z= 0.128 Angle : 0.614 8.471 26421 Z= 0.315 Chirality : 0.044 0.187 3126 Planarity : 0.004 0.037 3243 Dihedral : 4.820 26.971 2473 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.65 % Allowed : 11.76 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2265 helix: 0.49 (0.29), residues: 369 sheet: 0.36 (0.18), residues: 798 loop : -0.09 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 94 TYR 0.022 0.002 TYR A 39 PHE 0.012 0.002 PHE C 376 TRP 0.016 0.001 TRP I 628 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (19257) covalent geometry : angle 0.59380 / 0.31 (26157) SS BOND : bond 0.00179 / 0.13 ( 42) SS BOND : angle 0.81268 / 0.56 ( 84) hydrogen bonds : bond 0.04357 / 2.93 ( 672) hydrogen bonds : angle 5.66650 / 3.92 ( 1800) link_BETA1-4 : bond 0.00572 / 0.34 ( 18) link_BETA1-4 : angle 1.57123 / 1.08 ( 54) link_NAG-ASN : bond 0.00376 / 0.27 ( 42) link_NAG-ASN : angle 2.10890 / 1.46 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.739 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 150 MET cc_start: 0.7396 (mmm) cc_final: 0.7085 (mmt) REVERT: B 530 MET cc_start: 0.6405 (mpp) cc_final: 0.6106 (mpp) REVERT: B 535 MET cc_start: 0.7823 (mmm) cc_final: 0.7409 (mmm) REVERT: B 610 TRP cc_start: 0.8164 (t-100) cc_final: 0.7889 (t-100) REVERT: B 626 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7304 (mtt) REVERT: B 627 THR cc_start: 0.7123 (t) cc_final: 0.6890 (t) REVERT: B 648 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7996 (pt0) REVERT: B 649 SER cc_start: 0.9322 (m) cc_final: 0.8929 (t) REVERT: B 650 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8114 (tp40) REVERT: C 39 TYR cc_start: 0.8305 (m-80) cc_final: 0.7777 (m-10) REVERT: D 535 MET cc_start: 0.7335 (mmm) cc_final: 0.6347 (mmm) REVERT: D 593 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7401 (mp) REVERT: D 617 ARG cc_start: 0.7121 (mtp-110) cc_final: 0.6816 (mtp-110) REVERT: D 634 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8604 (mm-30) REVERT: D 648 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8211 (pt0) REVERT: D 650 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: F 91 THR cc_start: 0.8581 (p) cc_final: 0.8223 (p) REVERT: G 161 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6220 (ttt) REVERT: G 427 TRP cc_start: 0.7242 (m-10) cc_final: 0.6399 (m-90) REVERT: I 610 TRP cc_start: 0.8129 (t-100) cc_final: 0.7670 (t-100) REVERT: I 648 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8109 (pt0) REVERT: I 650 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: I 651 ASN cc_start: 0.6226 (p0) cc_final: 0.6007 (p0) REVERT: K 69 THR cc_start: 0.8602 (p) cc_final: 0.8316 (p) outliers start: 53 outliers final: 32 residues processed: 358 average time/residue: 0.1506 time to fit residues: 81.5248 Evaluate side-chains 325 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 164 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 224 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 208 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN C 195 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098376 restraints weight = 32880.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.100993 restraints weight = 21020.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102769 restraints weight = 15438.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103948 restraints weight = 12458.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104815 restraints weight = 10691.903| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19359 Z= 0.152 Angle : 0.620 7.604 26421 Z= 0.319 Chirality : 0.045 0.176 3126 Planarity : 0.004 0.037 3243 Dihedral : 4.776 27.276 2469 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.90 % Allowed : 13.11 % Favored : 83.98 % 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: 0.14 (0.18), residues: 2265 helix: 0.43 (0.29), residues: 369 sheet: 0.38 (0.18), residues: 798 loop : -0.12 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 617 TYR 0.029 0.002 TYR I 586 PHE 0.017 0.002 PHE C 376 TRP 0.016 0.001 TRP I 628 HIS 0.004 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (19257) covalent geometry : angle 0.60123 / 0.32 (26157) SS BOND : bond 0.00261 / 0.18 ( 42) SS BOND : angle 1.03641 / 0.70 ( 84) hydrogen bonds : bond 0.04252 / 2.87 ( 672) hydrogen bonds : angle 5.58892 / 3.88 ( 1800) link_BETA1-4 : bond 0.00480 / 0.30 ( 18) link_BETA1-4 : angle 1.44776 / 1.02 ( 54) link_NAG-ASN : bond 0.00304 / 0.22 ( 42) link_NAG-ASN : angle 2.01285 / 1.39 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 296 time to evaluate : 0.711 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: B 626 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7217 (mtt) REVERT: B 627 THR cc_start: 0.7282 (t) cc_final: 0.6991 (t) REVERT: B 634 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8326 (mm-30) REVERT: B 648 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7977 (pt0) REVERT: B 649 SER cc_start: 0.9229 (m) cc_final: 0.8869 (t) REVERT: B 650 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: L 46 LEU cc_start: 0.7965 (tt) cc_final: 0.7727 (tt) REVERT: C 39 TYR cc_start: 0.8361 (m-80) cc_final: 0.7779 (m-10) REVERT: C 150 MET cc_start: 0.7017 (mmt) cc_final: 0.6667 (mmt) REVERT: D 593 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7491 (mp) REVERT: D 617 ARG cc_start: 0.7280 (mtp-110) cc_final: 0.6941 (mtp-110) REVERT: D 648 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8056 (pt0) REVERT: D 650 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8239 (tp40) REVERT: F 91 THR cc_start: 0.8696 (p) cc_final: 0.8319 (p) REVERT: G 150 MET cc_start: 0.6976 (mmm) cc_final: 0.6603 (mtt) REVERT: G 427 TRP cc_start: 0.7300 (m-10) cc_final: 0.6437 (m-90) REVERT: I 607 ASN cc_start: 0.8212 (m-40) cc_final: 0.7717 (m110) REVERT: I 610 TRP cc_start: 0.8271 (t-100) cc_final: 0.7723 (t-100) REVERT: I 650 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: I 656 ASN cc_start: 0.7088 (OUTLIER) cc_final: 0.6804 (m110) REVERT: J 110 THR cc_start: 0.7118 (m) cc_final: 0.6906 (m) REVERT: K 69 THR cc_start: 0.8641 (p) cc_final: 0.8280 (p) outliers start: 58 outliers final: 38 residues processed: 326 average time/residue: 0.1515 time to fit residues: 74.9779 Evaluate side-chains 304 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain I residue 656 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 3 optimal weight: 0.0970 chunk 68 optimal weight: 3.9990 chunk 140 optimal weight: 0.0010 chunk 137 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 618 ASN ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099302 restraints weight = 32643.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.101951 restraints weight = 20937.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103783 restraints weight = 15334.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105063 restraints weight = 12274.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.105970 restraints weight = 10428.609| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19359 Z= 0.121 Angle : 0.600 7.260 26421 Z= 0.305 Chirality : 0.044 0.170 3126 Planarity : 0.004 0.035 3243 Dihedral : 4.623 26.081 2469 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.45 % Allowed : 14.01 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2265 helix: 0.33 (0.29), residues: 369 sheet: 0.48 (0.19), residues: 759 loop : -0.08 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 617 TYR 0.018 0.001 TYR D 586 PHE 0.011 0.001 PHE C 376 TRP 0.031 0.001 TRP B 628 HIS 0.003 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (19257) covalent geometry : angle 0.58318 / 0.30 (26157) SS BOND : bond 0.00200 / 0.15 ( 42) SS BOND : angle 0.81933 / 0.56 ( 84) hydrogen bonds : bond 0.04003 / 2.71 ( 672) hydrogen bonds : angle 5.47918 / 3.79 ( 1800) link_BETA1-4 : bond 0.00510 / 0.31 ( 18) link_BETA1-4 : angle 1.33143 / 0.93 ( 54) link_NAG-ASN : bond 0.00250 / 0.18 ( 42) link_NAG-ASN : angle 1.90180 / 1.32 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 282 time to evaluate : 0.510 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: B 545 LEU cc_start: 0.8561 (mt) cc_final: 0.8236 (mt) REVERT: B 610 TRP cc_start: 0.8158 (t-100) cc_final: 0.7751 (t-100) REVERT: B 628 TRP cc_start: 0.7821 (t-100) cc_final: 0.7560 (t-100) REVERT: B 634 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8384 (mm-30) REVERT: B 648 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7826 (pt0) REVERT: B 649 SER cc_start: 0.9275 (m) cc_final: 0.8913 (t) REVERT: B 650 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: C 39 TYR cc_start: 0.8415 (m-80) cc_final: 0.7780 (m-10) REVERT: C 150 MET cc_start: 0.6602 (mmt) cc_final: 0.6363 (mmt) REVERT: D 530 MET cc_start: 0.8076 (mmm) cc_final: 0.7686 (mmm) REVERT: D 593 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7500 (mp) REVERT: D 610 TRP cc_start: 0.8105 (t-100) cc_final: 0.7788 (t-100) REVERT: D 626 MET cc_start: 0.7670 (mtt) cc_final: 0.7422 (mtt) REVERT: D 634 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8429 (mm-30) REVERT: D 648 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8053 (pt0) REVERT: F 91 THR cc_start: 0.8647 (p) cc_final: 0.8240 (p) REVERT: G 427 TRP cc_start: 0.7309 (m-10) cc_final: 0.6421 (m-90) REVERT: I 607 ASN cc_start: 0.8203 (m-40) cc_final: 0.7814 (m-40) REVERT: I 610 TRP cc_start: 0.8369 (t-100) cc_final: 0.7803 (t-100) REVERT: I 617 ARG cc_start: 0.6717 (mtp-110) cc_final: 0.6366 (mtp-110) REVERT: I 656 ASN cc_start: 0.7790 (t0) cc_final: 0.7296 (m110) REVERT: J 110 THR cc_start: 0.7203 (m) cc_final: 0.6995 (m) REVERT: K 69 THR cc_start: 0.8613 (p) cc_final: 0.8233 (p) outliers start: 49 outliers final: 36 residues processed: 311 average time/residue: 0.1479 time to fit residues: 70.2670 Evaluate side-chains 302 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 19 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 656 ASN L 32 HIS ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN K 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094036 restraints weight = 33409.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096528 restraints weight = 21728.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098281 restraints weight = 16221.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099447 restraints weight = 13117.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100337 restraints weight = 11295.403| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19359 Z= 0.205 Angle : 0.673 10.160 26421 Z= 0.343 Chirality : 0.046 0.192 3126 Planarity : 0.004 0.041 3243 Dihedral : 4.956 32.438 2469 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.40 % Allowed : 15.02 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.18), residues: 2265 helix: 0.47 (0.29), residues: 345 sheet: 0.46 (0.19), residues: 759 loop : -0.36 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 151 TYR 0.019 0.002 TYR D 586 PHE 0.024 0.002 PHE C 376 TRP 0.022 0.002 TRP B 628 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (19257) covalent geometry : angle 0.65516 / 0.34 (26157) SS BOND : bond 0.00550 / 0.32 ( 42) SS BOND : angle 1.15559 / 0.72 ( 84) hydrogen bonds : bond 0.04575 / 3.10 ( 672) hydrogen bonds : angle 5.58535 / 3.86 ( 1800) link_BETA1-4 : bond 0.00442 / 0.27 ( 18) link_BETA1-4 : angle 1.35517 / 1.00 ( 54) link_NAG-ASN : bond 0.00347 / 0.24 ( 42) link_NAG-ASN : angle 2.03322 / 1.40 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 0.724 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: B 628 TRP cc_start: 0.8122 (t-100) cc_final: 0.7774 (t-100) REVERT: B 649 SER cc_start: 0.9353 (m) cc_final: 0.9052 (t) REVERT: B 650 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: C 39 TYR cc_start: 0.8516 (m-80) cc_final: 0.7909 (m-10) REVERT: D 593 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7641 (mp) REVERT: D 617 ARG cc_start: 0.7194 (mtp-110) cc_final: 0.6782 (mtp-110) REVERT: D 634 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8587 (mm-30) REVERT: D 648 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8007 (pt0) REVERT: G 427 TRP cc_start: 0.7284 (m-10) cc_final: 0.6453 (m-90) REVERT: I 607 ASN cc_start: 0.8331 (m-40) cc_final: 0.7871 (m-40) REVERT: I 617 ARG cc_start: 0.6995 (mtp-110) cc_final: 0.6667 (mtp-110) REVERT: I 627 THR cc_start: 0.8001 (t) cc_final: 0.7769 (t) REVERT: I 656 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7096 (m-40) REVERT: J 110 THR cc_start: 0.7357 (m) cc_final: 0.7139 (m) REVERT: K 69 THR cc_start: 0.8666 (p) cc_final: 0.8239 (p) outliers start: 48 outliers final: 44 residues processed: 313 average time/residue: 0.1492 time to fit residues: 70.8160 Evaluate side-chains 313 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 266 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain I residue 656 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 70 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 172 optimal weight: 0.0060 chunk 106 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 185 optimal weight: 0.0470 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 24 GLN C 99 ASN C 103 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097042 restraints weight = 33079.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099655 restraints weight = 21326.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101455 restraints weight = 15700.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102560 restraints weight = 12626.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.103510 restraints weight = 10875.502| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19359 Z= 0.123 Angle : 0.619 12.455 26421 Z= 0.312 Chirality : 0.044 0.168 3126 Planarity : 0.004 0.037 3243 Dihedral : 4.739 34.259 2469 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.35 % Allowed : 15.87 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2265 helix: 0.31 (0.29), residues: 363 sheet: 0.43 (0.19), residues: 777 loop : -0.27 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 617 TYR 0.021 0.001 TYR C 40 PHE 0.019 0.001 PHE L 98 TRP 0.031 0.001 TRP I 628 HIS 0.003 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (19257) covalent geometry : angle 0.60312 / 0.31 (26157) SS BOND : bond 0.00400 / 0.22 ( 42) SS BOND : angle 0.99055 / 0.63 ( 84) hydrogen bonds : bond 0.04040 / 2.74 ( 672) hydrogen bonds : angle 5.42638 / 3.74 ( 1800) link_BETA1-4 : bond 0.00454 / 0.27 ( 18) link_BETA1-4 : angle 1.25530 / 0.89 ( 54) link_NAG-ASN : bond 0.00213 / 0.15 ( 42) link_NAG-ASN : angle 1.88861 / 1.32 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 628 TRP cc_start: 0.7995 (t-100) cc_final: 0.7641 (t-100) REVERT: B 649 SER cc_start: 0.9341 (m) cc_final: 0.9053 (t) REVERT: B 650 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: L 48 ILE cc_start: 0.7369 (mm) cc_final: 0.7103 (mm) REVERT: C 39 TYR cc_start: 0.8457 (m-80) cc_final: 0.7855 (m-10) REVERT: C 427 TRP cc_start: 0.7089 (m-10) cc_final: 0.6712 (m-90) REVERT: D 530 MET cc_start: 0.8029 (mmm) cc_final: 0.7383 (mmm) REVERT: D 593 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7637 (mp) REVERT: D 610 TRP cc_start: 0.8039 (t-100) cc_final: 0.7683 (t-100) REVERT: D 634 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8551 (mm-30) REVERT: D 648 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8021 (pt0) REVERT: F 91 THR cc_start: 0.8713 (p) cc_final: 0.8319 (p) REVERT: G 427 TRP cc_start: 0.7286 (m-10) cc_final: 0.6494 (m-90) REVERT: I 607 ASN cc_start: 0.8466 (m-40) cc_final: 0.8020 (m-40) REVERT: I 617 ARG cc_start: 0.7053 (mtp-110) cc_final: 0.6846 (mtp-110) REVERT: I 656 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.6924 (m110) REVERT: J 110 THR cc_start: 0.7277 (m) cc_final: 0.7071 (m) REVERT: K 69 THR cc_start: 0.8606 (p) cc_final: 0.8274 (p) outliers start: 47 outliers final: 40 residues processed: 314 average time/residue: 0.1498 time to fit residues: 71.4798 Evaluate side-chains 308 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 656 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 217 optimal weight: 2.9990 chunk 176 optimal weight: 0.0070 chunk 6 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 640 GLN C 99 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.093367 restraints weight = 33463.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095936 restraints weight = 21727.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097714 restraints weight = 16092.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098929 restraints weight = 13012.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099761 restraints weight = 11192.609| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19359 Z= 0.202 Angle : 0.675 10.889 26421 Z= 0.343 Chirality : 0.045 0.166 3126 Planarity : 0.004 0.036 3243 Dihedral : 4.942 36.640 2469 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.35 % Allowed : 16.57 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 2265 helix: 0.20 (0.28), residues: 384 sheet: 0.38 (0.19), residues: 786 loop : -0.40 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 617 TYR 0.025 0.002 TYR B 586 PHE 0.021 0.002 PHE C 376 TRP 0.019 0.002 TRP C 479 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (19257) covalent geometry : angle 0.65653 / 0.34 (26157) SS BOND : bond 0.00378 / 0.25 ( 42) SS BOND : angle 1.48366 / 0.83 ( 84) hydrogen bonds : bond 0.04444 / 3.02 ( 672) hydrogen bonds : angle 5.47967 / 3.78 ( 1800) link_BETA1-4 : bond 0.00413 / 0.25 ( 18) link_BETA1-4 : angle 1.28658 / 0.93 ( 54) link_NAG-ASN : bond 0.00326 / 0.22 ( 42) link_NAG-ASN : angle 1.98930 / 1.39 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 266 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 601 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8717 (mtpp) REVERT: B 649 SER cc_start: 0.9316 (m) cc_final: 0.9072 (t) REVERT: B 650 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: L 48 ILE cc_start: 0.7490 (mm) cc_final: 0.7105 (mm) REVERT: C 39 TYR cc_start: 0.8540 (m-80) cc_final: 0.7884 (m-10) REVERT: D 593 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7718 (mp) REVERT: D 610 TRP cc_start: 0.8015 (t-100) cc_final: 0.7604 (t-100) REVERT: D 634 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8600 (mm-30) REVERT: D 648 GLU cc_start: 0.8709 (mm-30) cc_final: 0.7981 (pt0) REVERT: F 91 THR cc_start: 0.8715 (p) cc_final: 0.8324 (p) REVERT: G 427 TRP cc_start: 0.7319 (m-10) cc_final: 0.6472 (m-90) REVERT: I 607 ASN cc_start: 0.8455 (m-40) cc_final: 0.8044 (m-40) REVERT: I 656 ASN cc_start: 0.7747 (t0) cc_final: 0.7225 (m110) REVERT: J 23 LYS cc_start: 0.8082 (pttm) cc_final: 0.7805 (ptmt) REVERT: J 64 LYS cc_start: 0.9016 (tppt) cc_final: 0.8813 (tppt) outliers start: 47 outliers final: 44 residues processed: 300 average time/residue: 0.1409 time to fit residues: 64.2714 Evaluate side-chains 301 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 69 optimal weight: 0.0370 chunk 219 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS C 99 ASN C 130 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096947 restraints weight = 32957.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099535 restraints weight = 21058.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101307 restraints weight = 15433.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102499 restraints weight = 12408.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103405 restraints weight = 10626.339| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19359 Z= 0.123 Angle : 0.628 11.145 26421 Z= 0.316 Chirality : 0.044 0.156 3126 Planarity : 0.004 0.036 3243 Dihedral : 4.751 32.241 2469 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.10 % Allowed : 17.12 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2265 helix: 0.23 (0.28), residues: 384 sheet: 0.47 (0.19), residues: 780 loop : -0.37 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 617 TYR 0.023 0.001 TYR B 586 PHE 0.019 0.001 PHE G 376 TRP 0.086 0.002 TRP B 628 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (19257) covalent geometry : angle 0.61271 / 0.31 (26157) SS BOND : bond 0.00273 / 0.17 ( 42) SS BOND : angle 1.09177 / 0.66 ( 84) hydrogen bonds : bond 0.04042 / 2.76 ( 672) hydrogen bonds : angle 5.36577 / 3.70 ( 1800) link_BETA1-4 : bond 0.00575 / 0.35 ( 18) link_BETA1-4 : angle 1.19481 / 0.84 ( 54) link_NAG-ASN : bond 0.00205 / 0.14 ( 42) link_NAG-ASN : angle 1.82151 / 1.28 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 276 time to evaluate : 0.733 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: B 601 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8710 (mtpp) REVERT: B 607 ASN cc_start: 0.8592 (m110) cc_final: 0.7959 (m-40) REVERT: B 649 SER cc_start: 0.9315 (m) cc_final: 0.9111 (t) REVERT: B 650 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: C 39 TYR cc_start: 0.8488 (m-80) cc_final: 0.7853 (m-10) REVERT: C 427 TRP cc_start: 0.7039 (m-10) cc_final: 0.6791 (m-90) REVERT: D 530 MET cc_start: 0.7896 (mmm) cc_final: 0.7138 (mmm) REVERT: D 593 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7715 (mp) REVERT: D 607 ASN cc_start: 0.8371 (m-40) cc_final: 0.7928 (m110) REVERT: D 610 TRP cc_start: 0.8083 (t-100) cc_final: 0.7669 (t-100) REVERT: D 634 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8613 (mm-30) REVERT: D 647 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7486 (mm-30) REVERT: F 91 THR cc_start: 0.8729 (p) cc_final: 0.8357 (p) REVERT: G 427 TRP cc_start: 0.7261 (m-10) cc_final: 0.6497 (m-90) REVERT: I 607 ASN cc_start: 0.8429 (m-40) cc_final: 0.8005 (m-40) REVERT: I 617 ARG cc_start: 0.7116 (mtp-110) cc_final: 0.6767 (mtp-110) REVERT: I 656 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7116 (m-40) REVERT: J 23 LYS cc_start: 0.8067 (pttm) cc_final: 0.7680 (ptmt) REVERT: K 69 THR cc_start: 0.8451 (p) cc_final: 0.8109 (p) outliers start: 42 outliers final: 34 residues processed: 306 average time/residue: 0.1453 time to fit residues: 67.9152 Evaluate side-chains 290 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 253 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 656 ASN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 78 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 144 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096587 restraints weight = 33385.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099156 restraints weight = 21532.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100933 restraints weight = 15879.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102033 restraints weight = 12793.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103056 restraints weight = 11035.997| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19359 Z= 0.133 Angle : 0.634 10.563 26421 Z= 0.318 Chirality : 0.045 0.206 3126 Planarity : 0.004 0.038 3243 Dihedral : 4.685 29.524 2469 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.15 % Allowed : 17.77 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.18), residues: 2265 helix: 0.23 (0.28), residues: 384 sheet: 0.45 (0.19), residues: 792 loop : -0.36 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 151 TYR 0.023 0.002 TYR B 586 PHE 0.020 0.002 PHE G 376 TRP 0.102 0.002 TRP B 628 HIS 0.003 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (19257) covalent geometry : angle 0.61939 / 0.32 (26157) SS BOND : bond 0.00278 / 0.18 ( 42) SS BOND : angle 1.06313 / 0.64 ( 84) hydrogen bonds : bond 0.04028 / 2.75 ( 672) hydrogen bonds : angle 5.34226 / 3.69 ( 1800) link_BETA1-4 : bond 0.00433 / 0.26 ( 18) link_BETA1-4 : angle 1.14956 / 0.82 ( 54) link_NAG-ASN : bond 0.00277 / 0.22 ( 42) link_NAG-ASN : angle 1.80251 / 1.27 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3118.30 seconds wall clock time: 54 minutes 59.04 seconds (3299.04 seconds total)