Starting phenix.real_space_refine on Sat Sep 12 22:35:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x96_22102/09_2026/6x96_22102.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x96_22102/09_2026/6x96_22102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x96_22102/09_2026/6x96_22102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x96_22102/09_2026/6x96_22102.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6x96_22102/09_2026/6x96_22102.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x96_22102/09_2026/6x96_22102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x96_22102/09_2026/6x96_22102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x96_22102/09_2026/6x96_22102.map" } resolution = 3.4 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= 0.004 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 11865 2.51 5 N 3171 2.21 5 O 3747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 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: 18915 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3410 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 838 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3410 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 409} Chain breaks: 4 Chain: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 838 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "F" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "G" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3410 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 409} Chain breaks: 4 Chain: "I" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "J" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 838 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "G" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 4.32, per 1000 atoms: 0.23 Number of scatterers: 18915 At special positions: 0 Unit cell: (159.65, 152.44, 116.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 3747 8.00 N 3171 7.00 C 11865 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=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 35A" - pdb=" SG CYS E 50 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.09 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS J 35A" - pdb=" SG CYS J 50 " distance=2.03 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 ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 601 " - " ASN A 386 " " NAG A 602 " - " ASN A 363 " " NAG A 603 " - " ASN A 301 " " NAG A 614 " - " ASN A 295 " " NAG A 615 " - " ASN A 332 " " NAG A 616 " - " ASN A 392 " " NAG A 617 " - " ASN A 339 " " NAG A 618 " - " ASN A 133 " " NAG A 619 " - " ASN A 160 " " NAG A 620 " - " ASN A 197 " " NAG A 621 " - " ASN A 234 " " NAG C 601 " - " ASN C 386 " " NAG C 602 " - " ASN C 363 " " NAG C 603 " - " ASN C 301 " " NAG C 614 " - " ASN C 295 " " NAG C 615 " - " ASN C 332 " " NAG C 616 " - " ASN C 392 " " NAG C 617 " - " ASN C 339 " " NAG C 618 " - " ASN C 133 " " NAG C 619 " - " ASN C 160 " " NAG C 620 " - " ASN C 197 " " NAG C 621 " - " ASN C 234 " " NAG G 601 " - " ASN G 386 " " NAG G 602 " - " ASN G 363 " " NAG G 603 " - " ASN G 301 " " NAG G 614 " - " ASN G 295 " " NAG G 615 " - " ASN G 332 " " NAG G 616 " - " ASN G 392 " " NAG G 617 " - " ASN G 339 " " NAG G 618 " - " ASN G 133 " " NAG G 619 " - " ASN G 160 " " NAG G 620 " - " ASN G 197 " " NAG G 621 " - " ASN G 234 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 448 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN C 262 " " NAG R 1 " - " ASN C 448 " " NAG S 1 " - " ASN C 88 " " NAG T 1 " - " ASN C 156 " " NAG U 1 " - " ASN G 262 " " NAG V 1 " - " ASN G 448 " " NAG W 1 " - " ASN G 88 " " NAG X 1 " - " ASN G 156 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 801.0 milliseconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4278 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 42 sheets defined 21.6% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.193A 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 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.914A pdb=" N LEU A 483 " --> pdb=" O ARG A 480 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.303A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 652 Processing helix chain 'B' and resid 653 through 660 removed outlier: 3.651A pdb=" N ASN B 656 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP B 659 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.193A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 478 through 484 removed outlier: 3.914A pdb=" N LEU C 483 " --> pdb=" O ARG C 480 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 569 through 596 removed outlier: 4.304A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 652 Processing helix chain 'D' and resid 653 through 660 removed outlier: 3.652A pdb=" N ASN D 656 " --> pdb=" O GLN D 653 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP D 659 " --> pdb=" O ASN D 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 98 through 116 removed outlier: 4.193A 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 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 478 through 484 removed outlier: 3.914A pdb=" N LEU G 483 " --> pdb=" O ARG G 480 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR G 484 " --> pdb=" O SER G 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 536 through 542 Processing helix chain 'I' and resid 569 through 596 removed outlier: 4.304A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLN I 575 " --> pdb=" O TRP I 571 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU I 576 " --> pdb=" O GLY I 572 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 615 Processing helix chain 'I' and resid 618 through 625 Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 652 Processing helix chain 'I' and resid 653 through 660 removed outlier: 3.652A pdb=" N ASN I 656 " --> pdb=" O GLN I 653 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP I 659 " --> pdb=" O ASN I 656 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 55 No H-bonds generated for 'chain 'J' and resid 53 through 55' 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 498 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 53 through 55 removed outlier: 5.478A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.612A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.598A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.702A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.845A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 312 removed outlier: 7.050A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.073A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.682A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.553A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS L 88 " --> pdb=" O GLY L 100 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY L 100 " --> pdb=" O CYS L 88 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG L 90 " --> pdb=" O PHE L 98 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE L 98 " --> pdb=" O ARG L 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB7, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'C' and resid 53 through 55 removed outlier: 5.478A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AC1, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.612A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.598A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.702A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.109A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.845A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.109A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 301 through 312 removed outlier: 7.050A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AC7, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.073A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.682A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.554A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR F 102 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS F 88 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLY F 100 " --> pdb=" O CYS F 88 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG F 90 " --> pdb=" O PHE F 98 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE F 98 " --> pdb=" O ARG F 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 494 through 498 Processing sheet with id=AD3, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'G' and resid 53 through 55 removed outlier: 5.478A pdb=" N ILE G 215 " --> pdb=" O GLY G 250 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY G 250 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR G 217 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 92 through 94 Processing sheet with id=AD6, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.612A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.598A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.702A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.845A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 301 through 312 removed outlier: 7.050A pdb=" N ASN G 301 " --> pdb=" O ILE G 323 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE G 323 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.073A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 11 Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.682A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.554A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS K 88 " --> pdb=" O GLY K 100 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY K 100 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG K 90 " --> pdb=" O PHE K 98 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE K 98 " --> pdb=" O ARG K 90 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4540 1.33 - 1.46: 5941 1.46 - 1.60: 8592 1.60 - 1.73: 61 1.73 - 1.87: 165 Bond restraints: 19299 Sorted by residual: bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.406 -0.080 1.10e-02 8.26e+03 5.28e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.406 -0.080 1.10e-02 8.26e+03 5.26e+01 bond pdb=" NE ARG G 503 " pdb=" CZ ARG G 503 " ideal model delta sigma weight residual 1.326 1.406 -0.080 1.10e-02 8.26e+03 5.26e+01 bond pdb=" CB LEU H 4 " pdb=" CG LEU H 4 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CB LEU E 4 " pdb=" CG LEU E 4 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 19294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 22585 2.41 - 4.83: 3108 4.83 - 7.24: 448 7.24 - 9.65: 58 9.65 - 12.07: 9 Bond angle restraints: 26208 Sorted by residual: angle pdb=" C ILE E 48 " pdb=" CA ILE E 48 " pdb=" CB ILE E 48 " ideal model delta sigma weight residual 111.71 104.48 7.23 8.50e-01 1.38e+00 7.24e+01 angle pdb=" C ILE J 48 " pdb=" CA ILE J 48 " pdb=" CB ILE J 48 " ideal model delta sigma weight residual 111.71 104.49 7.22 8.50e-01 1.38e+00 7.22e+01 angle pdb=" C ILE H 48 " pdb=" CA ILE H 48 " pdb=" CB ILE H 48 " ideal model delta sigma weight residual 111.71 104.49 7.22 8.50e-01 1.38e+00 7.22e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.01 -8.45 1.02e+00 9.61e-01 6.86e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.98 -8.42 1.02e+00 9.61e-01 6.81e+01 ... (remaining 26203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 10599 17.91 - 35.82: 291 35.82 - 53.72: 90 53.72 - 71.63: 30 71.63 - 89.54: 21 Dihedral angle restraints: 11031 sinusoidal: 4374 harmonic: 6657 Sorted by residual: dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual 93.00 -179.91 -87.09 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 -179.91 -87.09 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 -179.93 -87.07 1 1.00e+01 1.00e-02 9.11e+01 ... (remaining 11028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2153 0.105 - 0.209: 645 0.209 - 0.314: 184 0.314 - 0.418: 102 0.418 - 0.523: 42 Chirality restraints: 3126 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.14e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.12e+02 ... (remaining 3123 not shown) Planarity restraints: 3291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 332 " 0.057 2.00e-02 2.50e+03 5.99e-02 4.48e+01 pdb=" CG ASN G 332 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN G 332 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN G 332 " -0.094 2.00e-02 2.50e+03 pdb=" C1 NAG G 615 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 332 " -0.057 2.00e-02 2.50e+03 5.98e-02 4.46e+01 pdb=" CG ASN C 332 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN C 332 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 332 " 0.094 2.00e-02 2.50e+03 pdb=" C1 NAG C 615 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 332 " -0.057 2.00e-02 2.50e+03 5.97e-02 4.46e+01 pdb=" CG ASN A 332 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 332 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 332 " 0.094 2.00e-02 2.50e+03 pdb=" C1 NAG A 615 " -0.072 2.00e-02 2.50e+03 ... (remaining 3288 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 6368 2.87 - 3.38: 16421 3.38 - 3.89: 31004 3.89 - 4.39: 35601 4.39 - 4.90: 57559 Nonbonded interactions: 146953 Sorted by model distance: nonbonded pdb=" N ASP C 477 " pdb=" O ASP C 477 " model vdw 2.363 2.496 nonbonded pdb=" N ASP G 477 " pdb=" O ASP G 477 " model vdw 2.364 2.496 nonbonded pdb=" N ASP A 477 " pdb=" O ASP A 477 " model vdw 2.364 2.496 nonbonded pdb=" NZ LYS G 46 " pdb=" OD2 ASP I 632 " model vdw 2.467 3.120 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.467 3.120 ... (remaining 146948 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: 0.05 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 'Q' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.550 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 0.133 19404 Z= 1.148 Angle : 1.762 12.065 26481 Z= 1.152 Chirality : 0.133 0.523 3126 Planarity : 0.008 0.033 3246 Dihedral : 10.214 89.541 6627 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2268 helix: -0.59 (0.25), residues: 357 sheet: 1.18 (0.19), residues: 687 loop : 1.00 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 90 TYR 0.038 0.008 TYR C 40 PHE 0.026 0.006 PHE H 91 TRP 0.044 0.009 TRP G 96 HIS 0.015 0.002 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.02169 / 1.13 (19299) covalent geometry : angle 1.73788 / 1.15 (26208) SS BOND : bond 0.02045 / 0.94 ( 42) SS BOND : angle 3.35467 / 2.24 ( 84) hydrogen bonds : bond 0.19471 / 12.87 ( 708) hydrogen bonds : angle 7.84014 / 5.48 ( 1836) link_ALPHA1-3 : bond 0.07847 / 3.93 ( 3) link_ALPHA1-3 : angle 3.91019 / 2.65 ( 9) link_BETA1-4 : bond 0.07567 / 4.21 ( 15) link_BETA1-4 : angle 4.55155 / 3.41 ( 45) link_NAG-ASN : bond 0.08210 / 5.34 ( 45) link_NAG-ASN : angle 2.74662 / 1.95 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 569 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: A 150 MET cc_start: 0.8334 (mmm) cc_final: 0.8056 (mmp) REVERT: L 33 LEU cc_start: 0.8420 (tp) cc_final: 0.7803 (tp) REVERT: L 72 THR cc_start: 0.7908 (m) cc_final: 0.7665 (m) REVERT: C 150 MET cc_start: 0.8219 (mmm) cc_final: 0.7959 (mmt) REVERT: D 627 THR cc_start: 0.7964 (p) cc_final: 0.7663 (p) REVERT: D 638 TYR cc_start: 0.7893 (m-80) cc_final: 0.7639 (m-10) REVERT: G 150 MET cc_start: 0.8310 (mmm) cc_final: 0.7935 (mmt) REVERT: I 627 THR cc_start: 0.7766 (p) cc_final: 0.7385 (p) REVERT: K 6 GLN cc_start: 0.6571 (tt0) cc_final: 0.6269 (tt0) REVERT: K 72 THR cc_start: 0.8028 (m) cc_final: 0.7356 (m) REVERT: K 92 TYR cc_start: 0.8249 (t80) cc_final: 0.7919 (t80) outliers start: 0 outliers final: 0 residues processed: 569 average time/residue: 0.1388 time to fit residues: 120.5595 Evaluate side-chains 366 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN B 591 GLN H 39 GLN L 37 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 302 ASN D 591 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN G 195 ASN I 591 GLN K 37 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088364 restraints weight = 30389.093| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.20 r_work: 0.2950 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19404 Z= 0.221 Angle : 0.811 11.423 26481 Z= 0.428 Chirality : 0.049 0.271 3126 Planarity : 0.005 0.034 3246 Dihedral : 5.390 22.692 2475 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.86 % Allowed : 9.27 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.70 (0.17), residues: 2268 helix: 0.29 (0.26), residues: 360 sheet: 1.01 (0.18), residues: 759 loop : 0.26 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 476 TYR 0.020 0.003 TYR B 638 PHE 0.031 0.003 PHE J 27 TRP 0.022 0.002 TRP G 112 HIS 0.007 0.002 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (19299) covalent geometry : angle 0.77718 / 0.42 (26208) SS BOND : bond 0.00512 / 0.39 ( 42) SS BOND : angle 1.45833 / 1.02 ( 84) hydrogen bonds : bond 0.06932 / 4.79 ( 708) hydrogen bonds : angle 6.08426 / 4.24 ( 1836) link_ALPHA1-3 : bond 0.00790 / 0.40 ( 3) link_ALPHA1-3 : angle 1.85347 / 1.12 ( 9) link_BETA1-4 : bond 0.00690 / 0.42 ( 15) link_BETA1-4 : angle 2.52509 / 1.84 ( 45) link_NAG-ASN : bond 0.00531 / 0.35 ( 45) link_NAG-ASN : angle 2.86436 / 2.03 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 373 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: A 180 ASP cc_start: 0.8523 (m-30) cc_final: 0.8243 (m-30) REVERT: A 355 ASN cc_start: 0.7345 (p0) cc_final: 0.7126 (p0) REVERT: A 444 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.6791 (tmm160) REVERT: B 621 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7748 (tt0) REVERT: B 624 ASP cc_start: 0.8423 (t0) cc_final: 0.7904 (m-30) REVERT: B 633 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8848 (tppt) REVERT: B 657 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6889 (pp20) REVERT: H 20 LEU cc_start: 0.8040 (mt) cc_final: 0.7775 (tp) REVERT: H 59 TYR cc_start: 0.6606 (m-80) cc_final: 0.6339 (m-80) REVERT: L 4 MET cc_start: 0.8325 (mmm) cc_final: 0.7862 (mmm) REVERT: L 21 ILE cc_start: 0.7204 (mm) cc_final: 0.6970 (mm) REVERT: L 33 LEU cc_start: 0.8736 (tp) cc_final: 0.8521 (tp) REVERT: L 39 LYS cc_start: 0.6584 (ttmm) cc_final: 0.6283 (mttm) REVERT: L 54 LEU cc_start: 0.8713 (pt) cc_final: 0.8495 (tp) REVERT: L 96 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7954 (p0) REVERT: C 67 ASN cc_start: 0.7523 (p0) cc_final: 0.7314 (p0) REVERT: C 173 TYR cc_start: 0.7739 (p90) cc_final: 0.7412 (p90) REVERT: C 230 ASP cc_start: 0.8300 (t0) cc_final: 0.8043 (t70) REVERT: C 355 ASN cc_start: 0.7525 (p0) cc_final: 0.7196 (p0) REVERT: C 482 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8010 (mm-30) REVERT: D 540 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.4980 (mp10) REVERT: D 633 LYS cc_start: 0.9109 (ttmm) cc_final: 0.8723 (tppt) REVERT: D 638 TYR cc_start: 0.7709 (m-80) cc_final: 0.7324 (m-10) REVERT: D 647 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6827 (mt-10) REVERT: D 657 GLU cc_start: 0.7688 (mm-30) cc_final: 0.6771 (pp20) REVERT: E 48 ILE cc_start: 0.8130 (mt) cc_final: 0.7609 (mt) REVERT: E 90 TYR cc_start: 0.5525 (m-80) cc_final: 0.5217 (m-10) REVERT: F 92 TYR cc_start: 0.8749 (t80) cc_final: 0.8443 (t80) REVERT: F 96 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.7335 (t0) REVERT: G 82 GLN cc_start: 0.7282 (pm20) cc_final: 0.6954 (tt0) REVERT: G 230 ASP cc_start: 0.8382 (t0) cc_final: 0.8067 (t70) REVERT: G 355 ASN cc_start: 0.7829 (p0) cc_final: 0.7510 (p0) REVERT: G 482 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8066 (mm-30) REVERT: I 621 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7929 (tt0) REVERT: I 625 ASN cc_start: 0.8086 (t0) cc_final: 0.7838 (t0) REVERT: I 633 LYS cc_start: 0.9153 (ttmm) cc_final: 0.8827 (tppt) REVERT: I 647 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6767 (mt-10) REVERT: I 657 GLU cc_start: 0.7598 (mm-30) cc_final: 0.6854 (pp20) REVERT: J 45 LEU cc_start: 0.8602 (mt) cc_final: 0.8348 (mt) REVERT: K 22 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8400 (mtpt) REVERT: K 92 TYR cc_start: 0.8327 (t80) cc_final: 0.7567 (t80) outliers start: 57 outliers final: 33 residues processed: 405 average time/residue: 0.1264 time to fit residues: 80.4465 Evaluate side-chains 362 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 323 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain I residue 569 THR Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 96 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 102 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 215 optimal weight: 30.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN L 91 ASN F 24 GLN F 37 GLN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN K 37 GLN K 91 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.122994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087304 restraints weight = 31071.736| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.91 r_work: 0.3023 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19404 Z= 0.226 Angle : 0.743 11.368 26481 Z= 0.382 Chirality : 0.048 0.285 3126 Planarity : 0.005 0.033 3246 Dihedral : 5.282 20.788 2475 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.06 % Allowed : 11.28 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.47 (0.17), residues: 2268 helix: 0.47 (0.26), residues: 360 sheet: 0.88 (0.18), residues: 777 loop : -0.06 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 476 TYR 0.019 0.002 TYR E 59 PHE 0.020 0.002 PHE J 27 TRP 0.030 0.002 TRP E 62 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (19299) covalent geometry : angle 0.71765 / 0.38 (26208) SS BOND : bond 0.00419 / 0.29 ( 42) SS BOND : angle 1.30046 / 0.90 ( 84) hydrogen bonds : bond 0.05856 / 3.99 ( 708) hydrogen bonds : angle 5.57071 / 3.89 ( 1836) link_ALPHA1-3 : bond 0.00645 / 0.32 ( 3) link_ALPHA1-3 : angle 1.35420 / 0.81 ( 9) link_BETA1-4 : bond 0.00469 / 0.28 ( 15) link_BETA1-4 : angle 1.55092 / 1.13 ( 45) link_NAG-ASN : bond 0.00351 / 0.25 ( 45) link_NAG-ASN : angle 2.50765 / 1.75 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 347 time to evaluate : 0.700 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 82 GLN cc_start: 0.8026 (tt0) cc_final: 0.7301 (pm20) REVERT: A 167 ASP cc_start: 0.9090 (t0) cc_final: 0.8764 (t0) REVERT: A 355 ASN cc_start: 0.7581 (p0) cc_final: 0.7299 (p0) REVERT: A 478 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6402 (t0) REVERT: B 588 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7371 (tmm-80) REVERT: B 621 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8005 (tt0) REVERT: B 624 ASP cc_start: 0.8478 (t0) cc_final: 0.7899 (m-30) REVERT: B 625 ASN cc_start: 0.8330 (t0) cc_final: 0.8086 (t0) REVERT: B 633 LYS cc_start: 0.9213 (ttmm) cc_final: 0.8896 (tppt) REVERT: B 657 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7104 (tm-30) REVERT: H 20 LEU cc_start: 0.8496 (mt) cc_final: 0.8199 (tp) REVERT: H 33 TYR cc_start: 0.6997 (m-10) cc_final: 0.6686 (m-80) REVERT: H 59 TYR cc_start: 0.7202 (m-80) cc_final: 0.6958 (m-80) REVERT: L 6 GLN cc_start: 0.6826 (tt0) cc_final: 0.6578 (mt0) REVERT: L 39 LYS cc_start: 0.6819 (ttmm) cc_final: 0.6618 (mttm) REVERT: L 54 LEU cc_start: 0.8839 (pt) cc_final: 0.8633 (tp) REVERT: C 173 TYR cc_start: 0.8107 (p90) cc_final: 0.7659 (p90) REVERT: C 230 ASP cc_start: 0.8722 (t0) cc_final: 0.8377 (t0) REVERT: C 268 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7389 (mm-30) REVERT: C 355 ASN cc_start: 0.7857 (p0) cc_final: 0.7618 (p0) REVERT: C 482 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8313 (mm-30) REVERT: D 543 ASN cc_start: 0.8887 (t0) cc_final: 0.8618 (t0) REVERT: D 588 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7492 (tpp-160) REVERT: D 633 LYS cc_start: 0.9236 (ttmm) cc_final: 0.8796 (tppt) REVERT: D 647 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: D 652 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7909 (tm-30) REVERT: E 59 TYR cc_start: 0.6797 (m-80) cc_final: 0.6171 (m-80) REVERT: E 90 TYR cc_start: 0.6226 (m-80) cc_final: 0.5937 (m-80) REVERT: F 6 GLN cc_start: 0.6208 (tt0) cc_final: 0.5832 (mt0) REVERT: G 230 ASP cc_start: 0.8538 (t0) cc_final: 0.8231 (t0) REVERT: G 268 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7469 (mm-30) REVERT: G 355 ASN cc_start: 0.8081 (p0) cc_final: 0.7847 (p0) REVERT: G 482 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8331 (mm-30) REVERT: I 588 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7618 (tpp-160) REVERT: I 621 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8050 (mp0) REVERT: I 633 LYS cc_start: 0.9266 (ttmm) cc_final: 0.8891 (tppt) REVERT: I 646 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7070 (mm) REVERT: I 647 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: I 657 GLU cc_start: 0.7779 (mm-30) cc_final: 0.6985 (pp20) REVERT: J 81 MET cc_start: 0.6250 (mtm) cc_final: 0.6045 (mtm) REVERT: K 48 ILE cc_start: 0.9168 (mm) cc_final: 0.8356 (tp) REVERT: K 53 LYS cc_start: 0.8497 (mtpp) cc_final: 0.8289 (mtpp) outliers start: 61 outliers final: 38 residues processed: 375 average time/residue: 0.1261 time to fit residues: 73.9958 Evaluate side-chains 373 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 331 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 646 LEU Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain K residue 95 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 38 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 78 optimal weight: 0.0020 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 ASN D 625 ASN F 24 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN G 195 ASN I 625 ASN K 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.126424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.089815 restraints weight = 31908.677| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 4.13 r_work: 0.3032 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19404 Z= 0.130 Angle : 0.648 12.276 26481 Z= 0.332 Chirality : 0.045 0.265 3126 Planarity : 0.004 0.032 3246 Dihedral : 4.989 19.387 2475 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.26 % Allowed : 12.88 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2268 helix: 0.84 (0.26), residues: 357 sheet: 0.81 (0.18), residues: 777 loop : -0.08 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 476 TYR 0.020 0.002 TYR L 49 PHE 0.016 0.002 PHE H 27 TRP 0.014 0.001 TRP E 62 HIS 0.007 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (19299) covalent geometry : angle 0.62441 / 0.33 (26208) SS BOND : bond 0.00533 / 0.41 ( 42) SS BOND : angle 1.10249 / 0.75 ( 84) hydrogen bonds : bond 0.04919 / 3.37 ( 708) hydrogen bonds : angle 5.23314 / 3.65 ( 1836) link_ALPHA1-3 : bond 0.00648 / 0.33 ( 3) link_ALPHA1-3 : angle 1.40101 / 0.85 ( 9) link_BETA1-4 : bond 0.00444 / 0.25 ( 15) link_BETA1-4 : angle 1.25552 / 0.92 ( 45) link_NAG-ASN : bond 0.00328 / 0.24 ( 45) link_NAG-ASN : angle 2.31546 / 1.62 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 358 time to evaluate : 0.680 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 82 GLN cc_start: 0.7999 (tt0) cc_final: 0.7255 (pm20) REVERT: A 167 ASP cc_start: 0.9094 (t0) cc_final: 0.8749 (t0) REVERT: A 268 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: A 355 ASN cc_start: 0.7559 (p0) cc_final: 0.7349 (p0) REVERT: B 588 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7299 (tmm-80) REVERT: B 621 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7962 (tt0) REVERT: B 624 ASP cc_start: 0.8427 (t0) cc_final: 0.7837 (m-30) REVERT: B 625 ASN cc_start: 0.8277 (t0) cc_final: 0.7815 (t0) REVERT: B 633 LYS cc_start: 0.9227 (ttmm) cc_final: 0.8923 (tppt) REVERT: B 657 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7038 (tm-30) REVERT: H 20 LEU cc_start: 0.8394 (mt) cc_final: 0.8103 (tp) REVERT: H 59 TYR cc_start: 0.7020 (m-80) cc_final: 0.6782 (m-80) REVERT: L 4 MET cc_start: 0.8199 (mmm) cc_final: 0.7840 (mmm) REVERT: L 21 ILE cc_start: 0.6843 (mp) cc_final: 0.6362 (mt) REVERT: L 22 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8233 (mmtp) REVERT: L 54 LEU cc_start: 0.8830 (pt) cc_final: 0.8612 (tp) REVERT: C 167 ASP cc_start: 0.9154 (t0) cc_final: 0.8860 (t0) REVERT: C 173 TYR cc_start: 0.7910 (p90) cc_final: 0.7454 (p90) REVERT: C 213 ILE cc_start: 0.8324 (mt) cc_final: 0.7972 (tp) REVERT: C 355 ASN cc_start: 0.7858 (p0) cc_final: 0.7602 (p0) REVERT: C 478 ASN cc_start: 0.7026 (OUTLIER) cc_final: 0.6260 (t0) REVERT: D 538 THR cc_start: 0.8763 (t) cc_final: 0.8445 (t) REVERT: D 543 ASN cc_start: 0.8826 (t0) cc_final: 0.8500 (t0) REVERT: D 588 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7375 (tpp-160) REVERT: D 624 ASP cc_start: 0.8240 (t0) cc_final: 0.7687 (m-30) REVERT: D 638 TYR cc_start: 0.8269 (m-10) cc_final: 0.7973 (m-10) REVERT: D 652 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7870 (tm-30) REVERT: E 59 TYR cc_start: 0.6421 (m-80) cc_final: 0.6015 (m-80) REVERT: E 90 TYR cc_start: 0.5869 (m-80) cc_final: 0.5643 (m-80) REVERT: F 6 GLN cc_start: 0.5897 (tt0) cc_final: 0.5450 (mt0) REVERT: F 22 LYS cc_start: 0.8422 (mmpt) cc_final: 0.8169 (mmpt) REVERT: G 213 ILE cc_start: 0.8083 (mt) cc_final: 0.7819 (tp) REVERT: G 355 ASN cc_start: 0.8022 (p0) cc_final: 0.7744 (p0) REVERT: G 478 ASN cc_start: 0.6848 (OUTLIER) cc_final: 0.6192 (t0) REVERT: I 543 ASN cc_start: 0.8220 (t0) cc_final: 0.7924 (t0) REVERT: I 588 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7338 (tmm-80) REVERT: I 621 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8077 (mp0) REVERT: I 633 LYS cc_start: 0.9224 (ttmm) cc_final: 0.8816 (tppt) REVERT: I 647 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: J 13 GLN cc_start: 0.7988 (pm20) cc_final: 0.7784 (pp30) REVERT: K 48 ILE cc_start: 0.9080 (mm) cc_final: 0.8251 (tp) REVERT: K 53 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7983 (mtpp) REVERT: K 92 TYR cc_start: 0.8974 (t80) cc_final: 0.8157 (t80) outliers start: 45 outliers final: 34 residues processed: 378 average time/residue: 0.1256 time to fit residues: 74.8380 Evaluate side-chains 377 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 339 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 655 LYS Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 21 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 224 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 210 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 114 GLN F 38 GLN K 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.124844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.089380 restraints weight = 31687.073| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.93 r_work: 0.3065 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19404 Z= 0.266 Angle : 0.742 12.324 26481 Z= 0.376 Chirality : 0.048 0.290 3126 Planarity : 0.005 0.044 3246 Dihedral : 5.152 20.282 2475 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.41 % Allowed : 12.93 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.33 (0.18), residues: 2268 helix: 0.62 (0.26), residues: 360 sheet: 0.75 (0.18), residues: 762 loop : -0.20 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 476 TYR 0.024 0.002 TYR F 92 PHE 0.018 0.002 PHE G 376 TRP 0.018 0.002 TRP J 36 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.27 (19299) covalent geometry : angle 0.71798 / 0.37 (26208) SS BOND : bond 0.00591 / 0.43 ( 42) SS BOND : angle 1.29204 / 0.92 ( 84) hydrogen bonds : bond 0.05702 / 3.87 ( 708) hydrogen bonds : angle 5.37757 / 3.75 ( 1836) link_ALPHA1-3 : bond 0.00535 / 0.27 ( 3) link_ALPHA1-3 : angle 1.47917 / 0.90 ( 9) link_BETA1-4 : bond 0.00363 / 0.21 ( 15) link_BETA1-4 : angle 1.29016 / 0.93 ( 45) link_NAG-ASN : bond 0.00406 / 0.27 ( 45) link_NAG-ASN : angle 2.49649 / 1.75 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 341 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8125 (tt0) cc_final: 0.7398 (pm20) REVERT: A 167 ASP cc_start: 0.9014 (t0) cc_final: 0.8662 (t0) REVERT: A 213 ILE cc_start: 0.8479 (mt) cc_final: 0.8107 (tp) REVERT: A 339 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7422 (t160) REVERT: A 355 ASN cc_start: 0.7707 (p0) cc_final: 0.7425 (p0) REVERT: B 540 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6093 (mp10) REVERT: B 588 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7483 (tmm-80) REVERT: B 624 ASP cc_start: 0.8506 (t0) cc_final: 0.7877 (m-30) REVERT: B 625 ASN cc_start: 0.8333 (t0) cc_final: 0.8118 (t0) REVERT: B 633 LYS cc_start: 0.9220 (ttmm) cc_final: 0.8827 (tppt) REVERT: B 657 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7211 (tm-30) REVERT: H 20 LEU cc_start: 0.8723 (mt) cc_final: 0.8433 (tp) REVERT: H 59 TYR cc_start: 0.7331 (m-80) cc_final: 0.7077 (m-80) REVERT: H 102 LEU cc_start: 0.8507 (tp) cc_final: 0.8142 (tt) REVERT: L 22 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8365 (mmtp) REVERT: C 82 GLN cc_start: 0.8365 (tt0) cc_final: 0.7538 (pm20) REVERT: C 173 TYR cc_start: 0.8340 (p90) cc_final: 0.7794 (p90) REVERT: C 213 ILE cc_start: 0.8692 (mt) cc_final: 0.8385 (tp) REVERT: C 230 ASP cc_start: 0.8915 (t0) cc_final: 0.8457 (t0) REVERT: C 355 ASN cc_start: 0.7935 (p0) cc_final: 0.7674 (p0) REVERT: D 543 ASN cc_start: 0.8926 (t0) cc_final: 0.8652 (t0) REVERT: D 588 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7585 (tpp-160) REVERT: D 617 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7507 (ttm170) REVERT: D 624 ASP cc_start: 0.8473 (t0) cc_final: 0.7909 (m-30) REVERT: D 633 LYS cc_start: 0.9198 (ttmm) cc_final: 0.8803 (tppt) REVERT: D 638 TYR cc_start: 0.8561 (m-10) cc_final: 0.8178 (m-10) REVERT: D 647 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: D 652 GLN cc_start: 0.8279 (tm-30) cc_final: 0.8029 (tm-30) REVERT: E 20 LEU cc_start: 0.8575 (mt) cc_final: 0.8242 (tp) REVERT: E 59 TYR cc_start: 0.7056 (m-80) cc_final: 0.6513 (m-80) REVERT: F 6 GLN cc_start: 0.6299 (tt0) cc_final: 0.5513 (mt0) REVERT: F 22 LYS cc_start: 0.8558 (mmpt) cc_final: 0.8353 (mmpt) REVERT: G 161 MET cc_start: 0.8613 (tpp) cc_final: 0.7902 (tpp) REVERT: G 213 ILE cc_start: 0.8490 (mt) cc_final: 0.8272 (tp) REVERT: G 230 ASP cc_start: 0.8776 (t0) cc_final: 0.8444 (t70) REVERT: G 355 ASN cc_start: 0.8117 (p0) cc_final: 0.7848 (p0) REVERT: I 588 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7618 (tmm-80) REVERT: I 621 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8103 (mp0) REVERT: I 633 LYS cc_start: 0.9231 (ttmm) cc_final: 0.8816 (tppt) REVERT: I 647 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: J 102 LEU cc_start: 0.8439 (tp) cc_final: 0.7982 (tt) REVERT: K 24 GLN cc_start: 0.7958 (tp-100) cc_final: 0.7705 (tp40) outliers start: 68 outliers final: 53 residues processed: 378 average time/residue: 0.1327 time to fit residues: 78.0505 Evaluate side-chains 381 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 324 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain K residue 95 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 214 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 143 optimal weight: 30.0000 chunk 182 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 219 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 91 ASN F 38 GLN ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.125064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.090196 restraints weight = 31362.912| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.86 r_work: 0.3094 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 19404 Z= 0.221 Angle : 0.715 13.691 26481 Z= 0.360 Chirality : 0.047 0.359 3126 Planarity : 0.004 0.040 3246 Dihedral : 5.131 20.612 2475 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.31 % Allowed : 13.18 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2268 helix: 0.67 (0.26), residues: 360 sheet: 0.64 (0.18), residues: 774 loop : -0.29 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 38 TYR 0.019 0.002 TYR L 49 PHE 0.012 0.002 PHE G 376 TRP 0.016 0.002 TRP E 62 HIS 0.006 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (19299) covalent geometry : angle 0.69087 / 0.35 (26208) SS BOND : bond 0.00516 / 0.38 ( 42) SS BOND : angle 1.25029 / 0.86 ( 84) hydrogen bonds : bond 0.05434 / 3.69 ( 708) hydrogen bonds : angle 5.30028 / 3.70 ( 1836) link_ALPHA1-3 : bond 0.00485 / 0.24 ( 3) link_ALPHA1-3 : angle 1.42214 / 0.86 ( 9) link_BETA1-4 : bond 0.00325 / 0.19 ( 15) link_BETA1-4 : angle 1.15279 / 0.83 ( 45) link_NAG-ASN : bond 0.00337 / 0.23 ( 45) link_NAG-ASN : angle 2.48636 / 1.77 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 337 time to evaluate : 0.700 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 82 GLN cc_start: 0.8174 (tt0) cc_final: 0.7426 (pm20) REVERT: A 161 MET cc_start: 0.8595 (tpp) cc_final: 0.8014 (tpp) REVERT: A 167 ASP cc_start: 0.9025 (t0) cc_final: 0.8651 (t0) REVERT: A 213 ILE cc_start: 0.8521 (mt) cc_final: 0.8166 (tp) REVERT: A 268 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7765 (tp30) REVERT: A 339 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7382 (t160) REVERT: A 355 ASN cc_start: 0.7767 (p0) cc_final: 0.7501 (p0) REVERT: B 540 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6107 (mp10) REVERT: B 588 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7480 (tmm-80) REVERT: B 601 LYS cc_start: 0.8355 (mmmm) cc_final: 0.8039 (mmmm) REVERT: B 624 ASP cc_start: 0.8485 (t0) cc_final: 0.7883 (m-30) REVERT: B 640 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7302 (mm-40) REVERT: B 647 GLU cc_start: 0.7827 (pm20) cc_final: 0.7228 (pt0) REVERT: H 20 LEU cc_start: 0.8680 (mt) cc_final: 0.8405 (tp) REVERT: H 33 TYR cc_start: 0.7136 (m-80) cc_final: 0.6455 (m-80) REVERT: H 59 TYR cc_start: 0.7331 (m-80) cc_final: 0.7083 (m-80) REVERT: L 4 MET cc_start: 0.8344 (mmm) cc_final: 0.7986 (mmm) REVERT: L 22 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8329 (mmtm) REVERT: L 53 LYS cc_start: 0.7962 (mtmm) cc_final: 0.7679 (mtmm) REVERT: C 82 GLN cc_start: 0.8390 (tt0) cc_final: 0.7517 (pm20) REVERT: C 173 TYR cc_start: 0.8393 (p90) cc_final: 0.7836 (p90) REVERT: C 213 ILE cc_start: 0.8711 (mt) cc_final: 0.8434 (tp) REVERT: C 230 ASP cc_start: 0.8928 (t0) cc_final: 0.8440 (t0) REVERT: C 355 ASN cc_start: 0.7919 (p0) cc_final: 0.7649 (p0) REVERT: D 540 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.5107 (mp10) REVERT: D 543 ASN cc_start: 0.9007 (t0) cc_final: 0.8734 (t0) REVERT: D 588 ARG cc_start: 0.7972 (ttm110) cc_final: 0.7538 (tpp-160) REVERT: D 617 ARG cc_start: 0.7889 (tpp80) cc_final: 0.7665 (ttm170) REVERT: D 624 ASP cc_start: 0.8446 (t0) cc_final: 0.7893 (m-30) REVERT: D 633 LYS cc_start: 0.9140 (ttmm) cc_final: 0.8682 (tppt) REVERT: D 647 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: D 652 GLN cc_start: 0.8313 (tm-30) cc_final: 0.8055 (tm-30) REVERT: D 657 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6794 (tm-30) REVERT: E 20 LEU cc_start: 0.8513 (mt) cc_final: 0.8198 (tp) REVERT: E 33 TYR cc_start: 0.7153 (m-80) cc_final: 0.6825 (m-80) REVERT: E 59 TYR cc_start: 0.7082 (m-80) cc_final: 0.6517 (m-80) REVERT: E 90 TYR cc_start: 0.4913 (m-80) cc_final: 0.4614 (m-10) REVERT: F 6 GLN cc_start: 0.6296 (tt0) cc_final: 0.5914 (mt0) REVERT: G 199 SER cc_start: 0.8923 (t) cc_final: 0.8719 (p) REVERT: G 213 ILE cc_start: 0.8519 (mt) cc_final: 0.8254 (tp) REVERT: G 230 ASP cc_start: 0.8846 (t0) cc_final: 0.8513 (t0) REVERT: G 355 ASN cc_start: 0.8083 (p0) cc_final: 0.7799 (p0) REVERT: I 588 ARG cc_start: 0.7989 (ttm110) cc_final: 0.7542 (tmm-80) REVERT: I 617 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7998 (ttm170) REVERT: I 633 LYS cc_start: 0.9240 (ttmm) cc_final: 0.8807 (tppt) REVERT: I 647 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7607 (mt-10) REVERT: J 102 LEU cc_start: 0.8354 (tp) cc_final: 0.7904 (tt) REVERT: K 24 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7692 (tp40) REVERT: K 48 ILE cc_start: 0.9219 (mm) cc_final: 0.8366 (tp) outliers start: 66 outliers final: 52 residues processed: 370 average time/residue: 0.1335 time to fit residues: 76.1549 Evaluate side-chains 382 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 323 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain I residue 617 ARG Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 655 LYS Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 95 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 61 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 204 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 24 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 ASN F 38 GLN ** I 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN K 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.127073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.092086 restraints weight = 31290.104| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.86 r_work: 0.3126 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19404 Z= 0.142 Angle : 0.663 14.555 26481 Z= 0.332 Chirality : 0.046 0.302 3126 Planarity : 0.004 0.074 3246 Dihedral : 4.942 20.186 2475 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.91 % Allowed : 14.29 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2268 helix: 1.13 (0.27), residues: 345 sheet: 0.78 (0.19), residues: 738 loop : -0.13 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 38 TYR 0.020 0.001 TYR L 49 PHE 0.013 0.001 PHE H 27 TRP 0.013 0.001 TRP E 62 HIS 0.007 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (19299) covalent geometry : angle 0.64102 / 0.33 (26208) SS BOND : bond 0.00427 / 0.33 ( 42) SS BOND : angle 1.11692 / 0.76 ( 84) hydrogen bonds : bond 0.04847 / 3.29 ( 708) hydrogen bonds : angle 5.10439 / 3.57 ( 1836) link_ALPHA1-3 : bond 0.00499 / 0.25 ( 3) link_ALPHA1-3 : angle 1.34133 / 0.81 ( 9) link_BETA1-4 : bond 0.00342 / 0.19 ( 15) link_BETA1-4 : angle 1.03651 / 0.74 ( 45) link_NAG-ASN : bond 0.00276 / 0.20 ( 45) link_NAG-ASN : angle 2.25627 / 1.60 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 342 time to evaluate : 0.705 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 82 GLN cc_start: 0.8190 (tt0) cc_final: 0.7404 (pm20) REVERT: A 167 ASP cc_start: 0.8997 (t0) cc_final: 0.8605 (t0) REVERT: A 213 ILE cc_start: 0.8573 (mt) cc_final: 0.8204 (tp) REVERT: A 268 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7795 (tp30) REVERT: A 339 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.7327 (t160) REVERT: A 355 ASN cc_start: 0.7751 (p0) cc_final: 0.7474 (p0) REVERT: B 536 THR cc_start: 0.7160 (OUTLIER) cc_final: 0.5917 (m) REVERT: B 540 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.5953 (mp10) REVERT: B 588 ARG cc_start: 0.7978 (ttm110) cc_final: 0.7614 (tpp-160) REVERT: B 624 ASP cc_start: 0.8469 (t0) cc_final: 0.7862 (m-30) REVERT: B 640 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7320 (mm-40) REVERT: B 654 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8880 (mm-30) REVERT: H 20 LEU cc_start: 0.8653 (mt) cc_final: 0.8376 (tp) REVERT: H 59 TYR cc_start: 0.7295 (m-80) cc_final: 0.7083 (m-80) REVERT: L 22 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8432 (tttm) REVERT: L 53 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7705 (mtmm) REVERT: C 82 GLN cc_start: 0.8356 (tt0) cc_final: 0.7496 (pm20) REVERT: C 161 MET cc_start: 0.8317 (tpp) cc_final: 0.7937 (tpp) REVERT: C 173 TYR cc_start: 0.8365 (p90) cc_final: 0.7843 (p90) REVERT: C 213 ILE cc_start: 0.8710 (mt) cc_final: 0.8444 (tp) REVERT: C 230 ASP cc_start: 0.8905 (t0) cc_final: 0.8419 (t70) REVERT: D 540 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.5123 (mp10) REVERT: D 543 ASN cc_start: 0.8999 (t0) cc_final: 0.8713 (t0) REVERT: D 588 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7535 (tpp-160) REVERT: D 617 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7077 (ttm170) REVERT: D 621 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: D 647 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: D 657 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6792 (tm-30) REVERT: E 20 LEU cc_start: 0.8538 (mt) cc_final: 0.8262 (tp) REVERT: E 33 TYR cc_start: 0.7180 (m-80) cc_final: 0.6884 (m-80) REVERT: E 59 TYR cc_start: 0.6977 (m-80) cc_final: 0.6538 (m-80) REVERT: E 86 ASP cc_start: 0.7939 (m-30) cc_final: 0.7732 (m-30) REVERT: F 6 GLN cc_start: 0.6208 (tt0) cc_final: 0.5489 (mt0) REVERT: G 161 MET cc_start: 0.8246 (tpp) cc_final: 0.7824 (tpp) REVERT: G 213 ILE cc_start: 0.8559 (mt) cc_final: 0.8304 (tp) REVERT: G 230 ASP cc_start: 0.8728 (t0) cc_final: 0.8395 (t0) REVERT: G 355 ASN cc_start: 0.8083 (p0) cc_final: 0.7792 (p0) REVERT: I 588 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7561 (tmm-80) REVERT: I 617 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7605 (ttm170) REVERT: I 624 ASP cc_start: 0.8431 (t0) cc_final: 0.7703 (m-30) REVERT: I 633 LYS cc_start: 0.9193 (ttmm) cc_final: 0.8759 (tppt) REVERT: I 647 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: J 33 TYR cc_start: 0.7199 (m-80) cc_final: 0.6954 (m-80) REVERT: J 102 LEU cc_start: 0.8194 (tp) cc_final: 0.7785 (tt) REVERT: K 24 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7497 (tp40) outliers start: 58 outliers final: 38 residues processed: 367 average time/residue: 0.1335 time to fit residues: 75.3894 Evaluate side-chains 375 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 328 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain I residue 617 ARG Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 655 LYS Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain K residue 95 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 121 optimal weight: 0.0370 chunk 165 optimal weight: 0.4980 chunk 181 optimal weight: 1.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN L 89 GLN ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN F 38 GLN ** I 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.128498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.094047 restraints weight = 30962.518| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.75 r_work: 0.3138 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19404 Z= 0.135 Angle : 0.671 14.609 26481 Z= 0.332 Chirality : 0.046 0.289 3126 Planarity : 0.004 0.043 3246 Dihedral : 4.858 20.351 2475 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.86 % Allowed : 14.89 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.48 (0.18), residues: 2268 helix: 0.98 (0.27), residues: 360 sheet: 0.62 (0.18), residues: 780 loop : -0.01 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 476 TYR 0.020 0.001 TYR F 49 PHE 0.011 0.001 PHE H 27 TRP 0.023 0.001 TRP I 631 HIS 0.006 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (19299) covalent geometry : angle 0.65162 / 0.33 (26208) SS BOND : bond 0.00422 / 0.32 ( 42) SS BOND : angle 1.11355 / 0.75 ( 84) hydrogen bonds : bond 0.04628 / 3.13 ( 708) hydrogen bonds : angle 5.07252 / 3.53 ( 1836) link_ALPHA1-3 : bond 0.00572 / 0.29 ( 3) link_ALPHA1-3 : angle 1.37513 / 0.83 ( 9) link_BETA1-4 : bond 0.00385 / 0.22 ( 15) link_BETA1-4 : angle 1.02178 / 0.73 ( 45) link_NAG-ASN : bond 0.00276 / 0.20 ( 45) link_NAG-ASN : angle 2.15110 / 1.52 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 337 time to evaluate : 0.636 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: A 82 GLN cc_start: 0.8224 (tt0) cc_final: 0.7456 (pm20) REVERT: A 167 ASP cc_start: 0.8955 (t0) cc_final: 0.8557 (t0) REVERT: A 213 ILE cc_start: 0.8620 (mt) cc_final: 0.8255 (tp) REVERT: A 268 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: A 339 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7365 (t160) REVERT: A 355 ASN cc_start: 0.7759 (p0) cc_final: 0.7478 (p0) REVERT: B 536 THR cc_start: 0.7193 (OUTLIER) cc_final: 0.6005 (m) REVERT: B 540 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6235 (mp10) REVERT: B 588 ARG cc_start: 0.7982 (ttm110) cc_final: 0.7617 (tpp-160) REVERT: B 624 ASP cc_start: 0.8407 (t0) cc_final: 0.7834 (m-30) REVERT: B 640 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7359 (mm-40) REVERT: B 647 GLU cc_start: 0.7836 (pm20) cc_final: 0.7234 (pt0) REVERT: B 654 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8863 (mm-30) REVERT: H 20 LEU cc_start: 0.8704 (mt) cc_final: 0.8407 (tp) REVERT: L 53 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7896 (mtmm) REVERT: C 82 GLN cc_start: 0.8364 (tt0) cc_final: 0.7490 (pm20) REVERT: C 161 MET cc_start: 0.8395 (tpp) cc_final: 0.8034 (tpp) REVERT: C 173 TYR cc_start: 0.8422 (p90) cc_final: 0.7924 (p90) REVERT: C 213 ILE cc_start: 0.8750 (mt) cc_final: 0.8481 (tp) REVERT: C 230 ASP cc_start: 0.8902 (t0) cc_final: 0.8416 (t70) REVERT: C 355 ASN cc_start: 0.7744 (p0) cc_final: 0.7453 (p0) REVERT: D 543 ASN cc_start: 0.8998 (t0) cc_final: 0.8693 (t0) REVERT: D 588 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7559 (tpp-160) REVERT: D 617 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7125 (ttm170) REVERT: D 621 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: D 647 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: D 657 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6833 (tm-30) REVERT: E 20 LEU cc_start: 0.8610 (mt) cc_final: 0.8312 (tp) REVERT: E 33 TYR cc_start: 0.7187 (m-80) cc_final: 0.6895 (m-80) REVERT: E 59 TYR cc_start: 0.6981 (m-80) cc_final: 0.6617 (m-80) REVERT: E 102 LEU cc_start: 0.8399 (tp) cc_final: 0.8150 (tp) REVERT: F 6 GLN cc_start: 0.6272 (tt0) cc_final: 0.5576 (mt0) REVERT: G 161 MET cc_start: 0.8305 (tpp) cc_final: 0.7793 (tpp) REVERT: G 213 ILE cc_start: 0.8617 (mt) cc_final: 0.8349 (tp) REVERT: G 230 ASP cc_start: 0.8722 (t0) cc_final: 0.8391 (t0) REVERT: G 355 ASN cc_start: 0.8095 (p0) cc_final: 0.7803 (p0) REVERT: I 588 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7630 (tmm-80) REVERT: I 633 LYS cc_start: 0.9198 (ttmm) cc_final: 0.8741 (tppt) REVERT: J 33 TYR cc_start: 0.7327 (m-80) cc_final: 0.7088 (m-80) REVERT: J 102 LEU cc_start: 0.8204 (tp) cc_final: 0.7859 (tt) REVERT: K 24 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7785 (tp40) outliers start: 57 outliers final: 40 residues processed: 362 average time/residue: 0.1302 time to fit residues: 73.9124 Evaluate side-chains 369 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 323 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain I residue 655 LYS Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain K residue 95 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 174 optimal weight: 6.9990 chunk 18 optimal weight: 0.0970 chunk 129 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 159 optimal weight: 0.0970 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN L 91 ASN D 540 GLN F 38 GLN K 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.127181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.092486 restraints weight = 31079.592| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.83 r_work: 0.3130 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19404 Z= 0.151 Angle : 0.685 14.619 26481 Z= 0.340 Chirality : 0.046 0.286 3126 Planarity : 0.004 0.041 3246 Dihedral : 4.873 25.790 2475 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.86 % Allowed : 15.09 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.43 (0.18), residues: 2268 helix: 1.30 (0.28), residues: 342 sheet: 0.54 (0.18), residues: 792 loop : -0.13 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 476 TYR 0.021 0.001 TYR F 49 PHE 0.010 0.001 PHE H 27 TRP 0.010 0.001 TRP D 623 HIS 0.006 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (19299) covalent geometry : angle 0.66598 / 0.34 (26208) SS BOND : bond 0.00458 / 0.33 ( 42) SS BOND : angle 1.27259 / 0.84 ( 84) hydrogen bonds : bond 0.04635 / 3.14 ( 708) hydrogen bonds : angle 5.05926 / 3.52 ( 1836) link_ALPHA1-3 : bond 0.00541 / 0.27 ( 3) link_ALPHA1-3 : angle 1.38392 / 0.84 ( 9) link_BETA1-4 : bond 0.00369 / 0.21 ( 15) link_BETA1-4 : angle 1.02185 / 0.73 ( 45) link_NAG-ASN : bond 0.00261 / 0.19 ( 45) link_NAG-ASN : angle 2.13235 / 1.52 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 346 time to evaluate : 0.691 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 82 GLN cc_start: 0.8207 (tt0) cc_final: 0.7423 (pm20) REVERT: A 150 MET cc_start: 0.8295 (mmp) cc_final: 0.8064 (tpt) REVERT: A 167 ASP cc_start: 0.8972 (t0) cc_final: 0.8523 (t0) REVERT: A 213 ILE cc_start: 0.8592 (mt) cc_final: 0.8223 (tp) REVERT: A 268 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7717 (tp30) REVERT: A 339 ASN cc_start: 0.7575 (OUTLIER) cc_final: 0.7355 (t160) REVERT: A 355 ASN cc_start: 0.7769 (p0) cc_final: 0.7477 (p0) REVERT: B 536 THR cc_start: 0.7118 (OUTLIER) cc_final: 0.5700 (m) REVERT: B 540 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6082 (mp10) REVERT: B 588 ARG cc_start: 0.7939 (ttm110) cc_final: 0.7568 (tpp-160) REVERT: B 624 ASP cc_start: 0.8468 (t0) cc_final: 0.7895 (m-30) REVERT: B 640 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7362 (mm-40) REVERT: B 654 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8854 (mm-30) REVERT: H 20 LEU cc_start: 0.8661 (mt) cc_final: 0.8355 (tp) REVERT: C 82 GLN cc_start: 0.8394 (tt0) cc_final: 0.7483 (pm20) REVERT: C 161 MET cc_start: 0.8376 (tpp) cc_final: 0.8032 (tpp) REVERT: C 173 TYR cc_start: 0.8443 (p90) cc_final: 0.7927 (p90) REVERT: C 213 ILE cc_start: 0.8710 (mt) cc_final: 0.8424 (tp) REVERT: C 230 ASP cc_start: 0.8922 (t0) cc_final: 0.8415 (t0) REVERT: D 543 ASN cc_start: 0.8982 (t0) cc_final: 0.8682 (t0) REVERT: D 588 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7513 (tpp-160) REVERT: D 617 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7098 (ttm170) REVERT: D 621 GLU cc_start: 0.7573 (mp0) cc_final: 0.7296 (pm20) REVERT: D 625 ASN cc_start: 0.8188 (t0) cc_final: 0.7642 (t0) REVERT: D 647 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7316 (pm20) REVERT: D 657 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6812 (tm-30) REVERT: E 20 LEU cc_start: 0.8586 (mt) cc_final: 0.8299 (tp) REVERT: E 33 TYR cc_start: 0.7164 (m-80) cc_final: 0.6830 (m-80) REVERT: E 59 TYR cc_start: 0.6940 (m-80) cc_final: 0.6552 (m-80) REVERT: E 102 LEU cc_start: 0.8267 (tp) cc_final: 0.8019 (tp) REVERT: F 6 GLN cc_start: 0.6157 (tt0) cc_final: 0.5394 (mt0) REVERT: G 213 ILE cc_start: 0.8561 (mt) cc_final: 0.8302 (tp) REVERT: G 230 ASP cc_start: 0.8749 (t0) cc_final: 0.8446 (t0) REVERT: G 355 ASN cc_start: 0.8101 (p0) cc_final: 0.7880 (p0) REVERT: I 588 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7596 (tmm-80) REVERT: J 13 GLN cc_start: 0.8408 (pp30) cc_final: 0.8105 (pp30) REVERT: J 33 TYR cc_start: 0.7296 (m-80) cc_final: 0.7081 (m-80) REVERT: J 102 LEU cc_start: 0.8185 (tp) cc_final: 0.7829 (tt) REVERT: K 24 GLN cc_start: 0.8021 (tp-100) cc_final: 0.7699 (tp40) REVERT: K 92 TYR cc_start: 0.9115 (t80) cc_final: 0.8494 (t80) outliers start: 57 outliers final: 45 residues processed: 374 average time/residue: 0.1281 time to fit residues: 74.9263 Evaluate side-chains 383 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 333 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain I residue 655 LYS Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain K residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 137 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 13 optimal weight: 0.0060 chunk 159 optimal weight: 0.0470 chunk 36 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.9896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN L 91 ASN G 348 GLN J 54 ASN K 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.128221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.093530 restraints weight = 31040.937| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.81 r_work: 0.3144 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19404 Z= 0.136 Angle : 0.692 14.718 26481 Z= 0.341 Chirality : 0.046 0.279 3126 Planarity : 0.004 0.038 3246 Dihedral : 4.869 26.204 2475 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 2.71 % Allowed : 15.44 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.52 (0.18), residues: 2268 helix: 1.39 (0.28), residues: 342 sheet: 0.70 (0.18), residues: 747 loop : -0.13 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 90 TYR 0.022 0.001 TYR L 49 PHE 0.010 0.001 PHE H 27 TRP 0.010 0.001 TRP D 623 HIS 0.007 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (19299) covalent geometry : angle 0.67285 / 0.34 (26208) SS BOND : bond 0.00392 / 0.31 ( 42) SS BOND : angle 1.46804 / 1.00 ( 84) hydrogen bonds : bond 0.04514 / 3.05 ( 708) hydrogen bonds : angle 5.01826 / 3.49 ( 1836) link_ALPHA1-3 : bond 0.00552 / 0.28 ( 3) link_ALPHA1-3 : angle 1.37468 / 0.83 ( 9) link_BETA1-4 : bond 0.00384 / 0.22 ( 15) link_BETA1-4 : angle 1.01097 / 0.72 ( 45) link_NAG-ASN : bond 0.00265 / 0.20 ( 45) link_NAG-ASN : angle 2.08403 / 1.48 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 348 time to evaluate : 0.718 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 82 GLN cc_start: 0.8234 (tt0) cc_final: 0.7437 (pm20) REVERT: A 150 MET cc_start: 0.8251 (mmp) cc_final: 0.8015 (tpt) REVERT: A 167 ASP cc_start: 0.8966 (t0) cc_final: 0.8517 (t0) REVERT: A 213 ILE cc_start: 0.8538 (mt) cc_final: 0.8184 (tp) REVERT: A 268 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: A 339 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.7323 (t160) REVERT: A 355 ASN cc_start: 0.7747 (p0) cc_final: 0.7444 (p0) REVERT: B 536 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.5873 (m) REVERT: B 540 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6193 (mp10) REVERT: B 588 ARG cc_start: 0.7903 (ttm110) cc_final: 0.7540 (tpp-160) REVERT: B 624 ASP cc_start: 0.8479 (t0) cc_final: 0.7863 (m-30) REVERT: B 640 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7375 (mm-40) REVERT: B 654 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8868 (mm-30) REVERT: H 20 LEU cc_start: 0.8646 (mt) cc_final: 0.8368 (tp) REVERT: H 35 MET cc_start: 0.7431 (mmt) cc_final: 0.7217 (mmp) REVERT: L 4 MET cc_start: 0.8465 (mmm) cc_final: 0.8140 (mmm) REVERT: C 82 GLN cc_start: 0.8388 (tt0) cc_final: 0.7453 (pm20) REVERT: C 161 MET cc_start: 0.8344 (tpp) cc_final: 0.7994 (tpp) REVERT: C 173 TYR cc_start: 0.8420 (p90) cc_final: 0.7902 (p90) REVERT: C 213 ILE cc_start: 0.8705 (mt) cc_final: 0.8392 (tp) REVERT: C 230 ASP cc_start: 0.8909 (t0) cc_final: 0.8441 (t70) REVERT: D 543 ASN cc_start: 0.8965 (t0) cc_final: 0.8662 (t0) REVERT: D 588 ARG cc_start: 0.7941 (ttm110) cc_final: 0.7493 (tpp-160) REVERT: D 617 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7060 (ttm170) REVERT: D 621 GLU cc_start: 0.7563 (mp0) cc_final: 0.7286 (pm20) REVERT: D 625 ASN cc_start: 0.8173 (t0) cc_final: 0.7700 (t0) REVERT: D 647 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: D 657 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6796 (tm-30) REVERT: E 20 LEU cc_start: 0.8599 (mt) cc_final: 0.8290 (tp) REVERT: E 33 TYR cc_start: 0.7098 (m-80) cc_final: 0.6806 (m-80) REVERT: E 59 TYR cc_start: 0.6904 (m-80) cc_final: 0.6580 (m-80) REVERT: E 102 LEU cc_start: 0.8237 (tp) cc_final: 0.8002 (tp) REVERT: F 6 GLN cc_start: 0.6129 (tt0) cc_final: 0.5380 (mt0) REVERT: F 49 TYR cc_start: 0.8031 (p90) cc_final: 0.7789 (p90) REVERT: G 161 MET cc_start: 0.8355 (tpp) cc_final: 0.8005 (tpp) REVERT: G 213 ILE cc_start: 0.8546 (mt) cc_final: 0.8288 (tp) REVERT: G 230 ASP cc_start: 0.8732 (t0) cc_final: 0.8399 (t0) REVERT: G 355 ASN cc_start: 0.8103 (p0) cc_final: 0.7886 (p0) REVERT: I 543 ASN cc_start: 0.8985 (m-40) cc_final: 0.8743 (t0) REVERT: I 588 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7580 (tmm-80) REVERT: J 102 LEU cc_start: 0.8123 (tp) cc_final: 0.7801 (tt) REVERT: K 24 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7782 (tp40) outliers start: 54 outliers final: 48 residues processed: 372 average time/residue: 0.1261 time to fit residues: 73.7815 Evaluate side-chains 389 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 339 ASN Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain I residue 655 LYS Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain K residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 13 optimal weight: 0.0070 chunk 38 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 0.0010 chunk 69 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN L 91 ASN J 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.128779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094106 restraints weight = 31185.772| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.83 r_work: 0.3125 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.287 19404 Z= 0.281 Angle : 1.049 59.193 26481 Z= 0.613 Chirality : 0.054 1.289 3126 Planarity : 0.005 0.138 3246 Dihedral : 4.894 26.080 2475 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 2.81 % Allowed : 15.89 % Favored : 81.30 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.12 % 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: 0.52 (0.18), residues: 2268 helix: 1.40 (0.28), residues: 342 sheet: 0.69 (0.18), residues: 747 loop : -0.13 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 94 TYR 0.020 0.001 TYR L 49 PHE 0.017 0.001 PHE F 62 TRP 0.009 0.001 TRP C 395 HIS 0.006 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.28 (19299) covalent geometry : angle 1.03609 / 0.61 (26208) SS BOND : bond 0.00389 / 0.31 ( 42) SS BOND : angle 1.99964 / 1.56 ( 84) hydrogen bonds : bond 0.04501 / 3.03 ( 708) hydrogen bonds : angle 5.01755 / 3.49 ( 1836) link_ALPHA1-3 : bond 0.00548 / 0.27 ( 3) link_ALPHA1-3 : angle 1.37766 / 0.84 ( 9) link_BETA1-4 : bond 0.00394 / 0.22 ( 15) link_BETA1-4 : angle 1.01753 / 0.73 ( 45) link_NAG-ASN : bond 0.00265 / 0.20 ( 45) link_NAG-ASN : angle 2.07754 / 1.47 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4016.48 seconds wall clock time: 69 minutes 51.20 seconds (4191.20 seconds total)