Starting phenix.real_space_refine on Mon Oct 26 09:15:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6orq_20178/10_2026/6orq_20178.cif Found real_map, /net/cci-nas-00/data/ceres_data/6orq_20178/10_2026/6orq_20178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6orq_20178/10_2026/6orq_20178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6orq_20178/10_2026/6orq_20178.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6orq_20178/10_2026/6orq_20178.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6orq_20178/10_2026/6orq_20178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6orq_20178/10_2026/6orq_20178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6orq_20178/10_2026/6orq_20178.map" } resolution = 4.4 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= -0.000 sd= 0.144 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 12626 2.51 5 N 3364 2.21 5 O 4054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20176 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "J" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "e" 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: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.61, per 1000 atoms: 0.23 Number of scatterers: 20176 At special positions: 0 Unit cell: (146.472, 145.036, 162.268, 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 4054 8.00 N 3364 7.00 C 12626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.05 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.07 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.05 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.06 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.06 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 160 " " NAG B 615 " - " ASN B 295 " " NAG B 616 " - " ASN B 301 " " NAG B 619 " - " ASN B 339 " " NAG B 620 " - " ASN B 355 " " NAG B 623 " - " ASN B 392 " " NAG B 624 " - " ASN B 448 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 611 " - " ASN G 295 " " NAG G 617 " - " ASN G 339 " " NAG G 618 " - " ASN G 355 " " NAG G 621 " - " ASN G 392 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 160 " " NAG I 614 " - " ASN I 295 " " NAG I 615 " - " ASN I 301 " " NAG I 619 " - " ASN I 339 " " NAG I 620 " - " ASN I 355 " " NAG I 623 " - " ASN I 392 " " NAG M 1 " - " ASN B 197 " " NAG N 1 " - " ASN B 234 " " NAG O 1 " - " ASN B 262 " " NAG P 1 " - " ASN B 279 " " NAG Q 1 " - " ASN B 332 " " NAG R 1 " - " ASN B 386 " " NAG S 1 " - " ASN G 160 " " NAG T 1 " - " ASN G 234 " " NAG U 1 " - " ASN G 262 " " NAG V 1 " - " ASN G 279 " " NAG W 1 " - " ASN G 301 " " NAG X 1 " - " ASN G 332 " " NAG Y 1 " - " ASN G 386 " " NAG Z 1 " - " ASN G 448 " " NAG a 1 " - " ASN G 197 " " NAG b 1 " - " ASN I 197 " " NAG c 1 " - " ASN I 234 " " NAG d 1 " - " ASN I 262 " " NAG e 1 " - " ASN I 279 " " NAG f 1 " - " ASN I 332 " " NAG g 1 " - " ASN I 386 " " NAG h 1 " - " ASN I 448 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 51 sheets defined 20.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 529 through 535 removed outlier: 3.743A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.965A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 590 " --> pdb=" O TYR A 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.757A pdb=" N THR B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 99 through 117 removed outlier: 3.876A pdb=" N ILE B 108 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.536A pdb=" N ASN B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 334 through 351 removed outlier: 3.513A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.997A pdb=" N VAL B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.668A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.771A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 535 removed outlier: 3.743A pdb=" N MET C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.966A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 590 " --> pdb=" O TYR C 586 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 591 " --> pdb=" O LEU C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 657 Processing helix chain 'C' and resid 657 through 662 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.816A pdb=" N ALA E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.742A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.966A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN F 591 " --> pdb=" O LEU F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 624 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 657 Processing helix chain 'F' and resid 657 through 662 Processing helix chain 'G' and resid 59 through 64 removed outlier: 3.908A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.616A pdb=" N ILE G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 139 removed outlier: 3.554A pdb=" N ASN G 137 " --> pdb=" O TYR G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 334 through 350 removed outlier: 3.522A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 removed outlier: 4.280A pdb=" N GLY G 354 " --> pdb=" O LYS G 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 351 through 354' Processing helix chain 'G' and resid 368 through 373 removed outlier: 4.087A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.570A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 475 through 483 removed outlier: 3.940A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 removed outlier: 3.796A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.777A pdb=" N ILE I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 139 removed outlier: 3.552A pdb=" N ASN I 137 " --> pdb=" O TYR I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 334 through 350 removed outlier: 3.503A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 354 removed outlier: 4.259A pdb=" N GLY I 354 " --> pdb=" O LYS I 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 351 through 354' Processing helix chain 'I' and resid 368 through 372 removed outlier: 4.028A pdb=" N VAL I 371 " --> pdb=" O ASP I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 390 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.726A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 425 through 429' Processing helix chain 'I' and resid 475 through 481 removed outlier: 3.974A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.816A pdb=" N ALA K 83 " --> pdb=" O GLU K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.817A pdb=" N ALA L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.877A pdb=" N CYS A 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR A 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 35 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.818A pdb=" N LYS B 490 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 131 removed outlier: 4.046A pdb=" N GLN B 130 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 158 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AA7, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.582A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.097A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 452 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 286 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.097A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 295 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 297 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 305 through 308 removed outlier: 3.533A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.601A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.949A pdb=" N CYS C 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA D 93 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB8, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB9, first strand: chain 'E' and resid 63 through 64 removed outlier: 3.973A pdb=" N SER E 63 " --> pdb=" O ASN E 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 74 " --> pdb=" O SER E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 603 through 609 removed outlier: 3.908A pdb=" N CYS F 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL I 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR F 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.524A pdb=" N LYS G 46 " --> pdb=" O LYS G 490 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS G 490 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AC5, first strand: chain 'G' and resid 130 through 132 removed outlier: 4.057A pdb=" N GLN G 130 " --> pdb=" O SER G 158 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER G 158 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR G 132 " --> pdb=" O GLN G 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC7, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC8, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.706A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AD1, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.731A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 304 through 308 removed outlier: 3.678A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 394 through 395 removed outlier: 3.597A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AD5, first strand: chain 'H' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.737A pdb=" N LYS I 490 " --> pdb=" O LYS I 46 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 53 through 55 removed outlier: 3.790A pdb=" N HIS I 216 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 91 through 93 removed outlier: 4.087A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 121 through 122 removed outlier: 3.947A pdb=" N LEU I 122 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE I 201 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 130 through 132 removed outlier: 4.110A pdb=" N GLN I 130 " --> pdb=" O SER I 158 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER I 158 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 160 through 162 Processing sheet with id=AE3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'I' and resid 271 through 274 removed outlier: 3.574A pdb=" N GLN I 287 " --> pdb=" O ILE I 271 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.741A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR I 297 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 304 through 308 removed outlier: 3.553A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 394 through 395 removed outlier: 3.623A pdb=" N ILE I 359 " --> pdb=" O TRP I 395 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 19 through 21 Processing sheet with id=AE9, first strand: chain 'J' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 45 through 46 Processing sheet with id=AF2, first strand: chain 'K' and resid 48 through 49 Processing sheet with id=AF3, first strand: chain 'K' and resid 63 through 64 removed outlier: 3.974A pdb=" N SER K 63 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN K 74 " --> pdb=" O SER K 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AF5, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AF6, first strand: chain 'L' and resid 63 through 64 removed outlier: 3.974A pdb=" N SER L 63 " --> pdb=" O ASN L 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 415 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3261 1.31 - 1.45: 5847 1.45 - 1.58: 11293 1.58 - 1.72: 0 1.72 - 1.85: 186 Bond restraints: 20587 Sorted by residual: bond pdb=" C3 NAG a 1 " pdb=" C4 NAG a 1 " ideal model delta sigma weight residual 1.524 1.449 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C3 BMA d 3 " pdb=" O3 BMA d 3 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C4 NAG a 1 " pdb=" C5 NAG a 1 " ideal model delta sigma weight residual 1.532 1.463 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C3 NAG a 2 " pdb=" C4 NAG a 2 " ideal model delta sigma weight residual 1.524 1.455 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C7 NAG a 1 " pdb=" C8 NAG a 1 " ideal model delta sigma weight residual 1.509 1.443 0.066 2.00e-02 2.50e+03 1.07e+01 ... (remaining 20582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 27272 3.58 - 7.16: 552 7.16 - 10.75: 92 10.75 - 14.33: 9 14.33 - 17.91: 9 Bond angle restraints: 27934 Sorted by residual: angle pdb=" N LEU J 45 " pdb=" CA LEU J 45 " pdb=" C LEU J 45 " ideal model delta sigma weight residual 110.80 125.23 -14.43 2.13e+00 2.20e-01 4.59e+01 angle pdb=" N LEU H 45 " pdb=" CA LEU H 45 " pdb=" C LEU H 45 " ideal model delta sigma weight residual 110.80 125.22 -14.42 2.13e+00 2.20e-01 4.58e+01 angle pdb=" N LEU D 45 " pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 110.80 125.19 -14.39 2.13e+00 2.20e-01 4.57e+01 angle pdb=" C3 NAG a 1 " pdb=" C2 NAG a 1 " pdb=" N2 NAG a 1 " ideal model delta sigma weight residual 110.74 92.83 17.91 3.00e+00 1.11e-01 3.56e+01 angle pdb=" N VAL B 371 " pdb=" CA VAL B 371 " pdb=" C VAL B 371 " ideal model delta sigma weight residual 113.42 106.98 6.44 1.17e+00 7.31e-01 3.03e+01 ... (remaining 27929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 10603 15.59 - 31.18: 763 31.18 - 46.77: 242 46.77 - 62.36: 48 62.36 - 77.96: 23 Dihedral angle restraints: 11679 sinusoidal: 4659 harmonic: 7020 Sorted by residual: dihedral pdb=" CA LYS J 13 " pdb=" C LYS J 13 " pdb=" N PRO J 14 " pdb=" CA PRO J 14 " ideal model delta harmonic sigma weight residual 180.00 -123.10 -56.90 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA LYS H 13 " pdb=" C LYS H 13 " pdb=" N PRO H 14 " pdb=" CA PRO H 14 " ideal model delta harmonic sigma weight residual 180.00 -123.14 -56.86 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LYS D 13 " pdb=" C LYS D 13 " pdb=" N PRO D 14 " pdb=" CA PRO D 14 " ideal model delta harmonic sigma weight residual -180.00 -123.15 -56.85 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 11676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 3213 0.166 - 0.333: 109 0.333 - 0.499: 11 0.499 - 0.666: 0 0.666 - 0.832: 4 Chirality restraints: 3337 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.65e+02 chirality pdb=" C5 NAG a 1 " pdb=" C4 NAG a 1 " pdb=" C6 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.41 -1.58 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 618 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.54e+01 ... (remaining 3334 not shown) Planarity restraints: 3514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.404 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" C7 NAG a 2 " 0.166 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.243 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.545 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 1 " 0.366 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C7 NAG a 1 " -0.127 2.00e-02 2.50e+03 pdb=" C8 NAG a 1 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG a 1 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG a 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.064 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO D 14 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.053 5.00e-02 4.00e+02 ... (remaining 3511 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 297 2.61 - 3.18: 17193 3.18 - 3.76: 30218 3.76 - 4.33: 37608 4.33 - 4.90: 59246 Nonbonded interactions: 144562 Sorted by model distance: nonbonded pdb=" O4 NAG a 2 " pdb=" O6 NAG a 2 " model vdw 2.039 3.040 nonbonded pdb=" O4 NAG a 1 " pdb=" O6 NAG a 1 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR J 68 " pdb=" O GLN J 81 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR H 68 " pdb=" O GLN H 81 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR D 68 " pdb=" O GLN D 81 " model vdw 2.243 3.040 ... (remaining 144557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'B' and resid 31 through 619) selection = chain 'G' selection = (chain 'I' and resid 31 through 619) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'O' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'X' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.620 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.008 0.075 20698 Z= 0.382 Angle : 1.390 25.597 28237 Z= 0.685 Chirality : 0.077 0.832 3337 Planarity : 0.011 0.332 3463 Dihedral : 12.609 77.955 7086 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.34 % Allowed : 16.29 % Favored : 83.38 % Rotamer: Outliers : 1.04 % Allowed : 7.81 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.61 % 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: -4.97 (0.13), residues: 2388 helix: -4.26 (0.15), residues: 288 sheet: -2.27 (0.23), residues: 459 loop : -3.69 (0.12), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 61 TYR 0.037 0.004 TYR I 134 PHE 0.023 0.003 PHE L 98 TRP 0.026 0.003 TRP I 35 HIS 0.013 0.003 HIS E 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00807 / 0.38 (20587) covalent geometry : angle 1.30914 / 0.67 (27934) SS BOND : bond 0.01467 / 1.06 ( 27) SS BOND : angle 2.13191 / 1.35 ( 54) hydrogen bonds : bond 0.32322 / 21.32 ( 414) hydrogen bonds : angle 9.35896 / 6.58 ( 1026) Misc. bond : bond 0.01549 / 0.82 ( 1) link_ALPHA1-3 : bond 0.01074 / 0.53 ( 2) link_ALPHA1-3 : angle 4.50965 / 2.50 ( 6) link_ALPHA1-6 : bond 0.00052 / 0.03 ( 2) link_ALPHA1-6 : angle 1.90239 / 0.99 ( 6) link_BETA1-4 : bond 0.00910 / 0.58 ( 28) link_BETA1-4 : angle 4.53708 / 3.02 ( 84) link_NAG-ASN : bond 0.00943 / 0.60 ( 51) link_NAG-ASN : angle 5.45183 / 3.64 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 618 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 540 GLN cc_start: 0.8982 (mp-120) cc_final: 0.8722 (mp10) REVERT: A 574 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8332 (mttm) REVERT: A 584 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 588 ARG cc_start: 0.9131 (ttt180) cc_final: 0.8894 (ttt90) REVERT: A 621 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8494 (tm-30) REVERT: A 647 GLU cc_start: 0.9051 (pp20) cc_final: 0.8848 (pp20) REVERT: A 648 GLU cc_start: 0.9036 (pp20) cc_final: 0.8704 (pp20) REVERT: A 654 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8770 (tp30) REVERT: B 80 ASN cc_start: 0.8902 (t0) cc_final: 0.8439 (p0) REVERT: B 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8595 (ttm) REVERT: B 114 GLN cc_start: 0.9278 (tm-30) cc_final: 0.9048 (tm-30) REVERT: B 161 MET cc_start: 0.9228 (tpp) cc_final: 0.8841 (tpp) REVERT: B 256 SER cc_start: 0.9266 (m) cc_final: 0.9009 (m) REVERT: B 340 GLU cc_start: 0.9317 (tp30) cc_final: 0.9107 (tp30) REVERT: C 535 MET cc_start: 0.8927 (mtt) cc_final: 0.8592 (mmm) REVERT: C 542 ARG cc_start: 0.9260 (mtp-110) cc_final: 0.9003 (ttp80) REVERT: C 543 ASN cc_start: 0.8918 (t0) cc_final: 0.8643 (t0) REVERT: C 574 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8783 (ttmm) REVERT: C 584 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 621 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 648 GLU cc_start: 0.9151 (pp20) cc_final: 0.8713 (pm20) REVERT: D 34 MET cc_start: 0.9026 (mpt) cc_final: 0.8781 (mmm) REVERT: D 36 TRP cc_start: 0.8331 (m100) cc_final: 0.8024 (m-10) REVERT: D 75 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8847 (mtpt) REVERT: D 82 LEU cc_start: 0.9165 (mt) cc_final: 0.8755 (mt) REVERT: D 85 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8659 (pp20) REVERT: E 37 GLN cc_start: 0.7675 (pp30) cc_final: 0.7096 (pp30) REVERT: E 38 GLN cc_start: 0.8843 (pt0) cc_final: 0.8462 (pt0) REVERT: E 72 THR cc_start: 0.7080 (t) cc_final: 0.6748 (t) REVERT: F 574 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8669 (ttmm) REVERT: F 584 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8485 (tm-30) REVERT: F 621 GLU cc_start: 0.8845 (tm-30) cc_final: 0.7487 (tm-30) REVERT: F 622 ILE cc_start: 0.9196 (pp) cc_final: 0.7976 (pp) REVERT: F 624 ASP cc_start: 0.8804 (m-30) cc_final: 0.8532 (m-30) REVERT: F 648 GLU cc_start: 0.9104 (pp20) cc_final: 0.8833 (pp20) REVERT: F 654 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8725 (tp30) REVERT: F 655 LYS cc_start: 0.8833 (pptt) cc_final: 0.8614 (pptt) REVERT: G 114 GLN cc_start: 0.9394 (tm-30) cc_final: 0.9115 (tm-30) REVERT: G 150 MET cc_start: 0.8892 (tmt) cc_final: 0.8542 (tmm) REVERT: G 161 MET cc_start: 0.9127 (tpp) cc_final: 0.8758 (tpp) REVERT: G 252 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8993 (mtpp) REVERT: G 302 ASN cc_start: 0.8304 (t0) cc_final: 0.7879 (t0) REVERT: G 321 ASP cc_start: 0.8678 (t70) cc_final: 0.8301 (t70) REVERT: H 1 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8389 (pm20) REVERT: H 29 PHE cc_start: 0.8894 (t80) cc_final: 0.8579 (t80) REVERT: H 51 ILE cc_start: 0.8556 (pt) cc_final: 0.8303 (pt) REVERT: H 67 PHE cc_start: 0.8728 (p90) cc_final: 0.8353 (p90) REVERT: I 80 ASN cc_start: 0.9034 (t0) cc_final: 0.8607 (p0) REVERT: I 114 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9088 (tm-30) REVERT: I 125 LEU cc_start: 0.8971 (tt) cc_final: 0.8686 (tt) REVERT: I 194 ILE cc_start: 0.9296 (tp) cc_final: 0.8974 (tp) REVERT: I 211 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8747 (tm-30) REVERT: I 217 TYR cc_start: 0.8111 (m-10) cc_final: 0.7031 (m-10) REVERT: I 230 ASP cc_start: 0.8785 (t0) cc_final: 0.8569 (t0) REVERT: I 252 LYS cc_start: 0.9348 (mtmm) cc_final: 0.8942 (mtpp) REVERT: I 340 GLU cc_start: 0.9287 (tp30) cc_final: 0.9014 (tm-30) REVERT: I 425 ASN cc_start: 0.9354 (p0) cc_final: 0.9099 (p0) REVERT: I 452 LEU cc_start: 0.9181 (mm) cc_final: 0.8444 (tt) REVERT: I 477 ASP cc_start: 0.9278 (p0) cc_final: 0.9075 (p0) REVERT: I 479 TRP cc_start: 0.8841 (m-10) cc_final: 0.8464 (m-10) REVERT: I 482 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8630 (mm-30) REVERT: J 1 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8244 (pm20) REVERT: J 27 PHE cc_start: 0.8394 (m-10) cc_final: 0.8029 (m-10) REVERT: J 29 PHE cc_start: 0.8710 (t80) cc_final: 0.8480 (t80) REVERT: J 34 MET cc_start: 0.9346 (mpt) cc_final: 0.9103 (mmm) REVERT: J 36 TRP cc_start: 0.8285 (m100) cc_final: 0.7885 (m100) REVERT: J 71 ARG cc_start: 0.8473 (tmt90) cc_final: 0.8150 (ttt-90) REVERT: J 82 LEU cc_start: 0.8863 (mt) cc_final: 0.8015 (mt) REVERT: J 83 LYS cc_start: 0.7458 (tppt) cc_final: 0.7237 (tppp) REVERT: J 85 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8408 (pp20) REVERT: J 91 TYR cc_start: 0.8743 (m-80) cc_final: 0.8534 (m-80) REVERT: K 37 GLN cc_start: 0.8014 (pp30) cc_final: 0.7190 (pp30) REVERT: K 38 GLN cc_start: 0.8597 (pt0) cc_final: 0.8307 (pp30) REVERT: K 45 LYS cc_start: 0.8632 (tptm) cc_final: 0.8256 (ttpt) REVERT: K 81 GLU cc_start: 0.9277 (pp20) cc_final: 0.8966 (pp20) REVERT: L 37 GLN cc_start: 0.8466 (pp30) cc_final: 0.7783 (pp30) REVERT: L 38 GLN cc_start: 0.8651 (pt0) cc_final: 0.8304 (pp30) REVERT: L 45 LYS cc_start: 0.8997 (tptm) cc_final: 0.8639 (ttpt) outliers start: 22 outliers final: 10 residues processed: 629 average time/residue: 0.1385 time to fit residues: 132.9728 Evaluate side-chains 435 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 422 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.0060 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 HIS A 590 GLN A 651 ASN B 66 HIS B 203 GLN B 258 GLN C 570 HIS C 590 GLN C 616 ASN C 651 ASN D 81 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS F 590 GLN F 616 ASN F 651 ASN G 66 HIS G 293 GLN G 300 ASN G 440 GLN H 81 GLN I 258 GLN J 81 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.088248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.070834 restraints weight = 64246.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.073212 restraints weight = 33925.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.074834 restraints weight = 21794.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.075943 restraints weight = 15881.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.076693 restraints weight = 12640.172| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20698 Z= 0.171 Angle : 0.952 19.340 28237 Z= 0.447 Chirality : 0.054 0.524 3337 Planarity : 0.006 0.092 3463 Dihedral : 7.721 45.117 2607 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.78 % Favored : 86.01 % Rotamer: Outliers : 0.52 % Allowed : 4.64 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.35 % 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: -4.40 (0.14), residues: 2388 helix: -2.57 (0.21), residues: 354 sheet: -1.53 (0.26), residues: 408 loop : -3.66 (0.12), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 178 TYR 0.023 0.002 TYR G 134 PHE 0.019 0.002 PHE B 376 TRP 0.018 0.002 TRP I 35 HIS 0.010 0.001 HIS K 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (20587) covalent geometry : angle 0.89575 / 0.43 (27934) SS BOND : bond 0.00510 / 0.30 ( 27) SS BOND : angle 1.95467 / 1.33 ( 54) hydrogen bonds : bond 0.06055 / 3.97 ( 414) hydrogen bonds : angle 6.35240 / 4.45 ( 1026) Misc. bond : bond 0.00079 / 0.04 ( 1) link_ALPHA1-3 : bond 0.01165 / 0.56 ( 2) link_ALPHA1-3 : angle 2.48182 / 1.36 ( 6) link_ALPHA1-6 : bond 0.00398 / 0.20 ( 2) link_ALPHA1-6 : angle 1.48637 / 0.78 ( 6) link_BETA1-4 : bond 0.00741 / 0.44 ( 28) link_BETA1-4 : angle 2.66168 / 1.78 ( 84) link_NAG-ASN : bond 0.00744 / 0.45 ( 51) link_NAG-ASN : angle 3.91888 / 2.56 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 573 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8735 (mmt) cc_final: 0.8532 (mmm) REVERT: A 584 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 617 ARG cc_start: 0.8643 (mtt180) cc_final: 0.7996 (mtm-85) REVERT: A 626 MET cc_start: 0.8306 (mtm) cc_final: 0.7631 (mtt) REVERT: A 648 GLU cc_start: 0.9067 (pp20) cc_final: 0.8752 (pp20) REVERT: B 80 ASN cc_start: 0.8860 (t0) cc_final: 0.8343 (p0) REVERT: B 98 ASN cc_start: 0.8441 (t0) cc_final: 0.6739 (t0) REVERT: B 99 ASN cc_start: 0.9227 (m-40) cc_final: 0.8581 (m-40) REVERT: B 102 GLU cc_start: 0.9278 (mp0) cc_final: 0.8804 (mp0) REVERT: B 114 GLN cc_start: 0.9310 (tm-30) cc_final: 0.9054 (tm-30) REVERT: B 321 ASP cc_start: 0.8931 (t70) cc_final: 0.8468 (t0) REVERT: B 452 LEU cc_start: 0.9429 (pt) cc_final: 0.8869 (pp) REVERT: C 584 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8480 (tm-30) REVERT: C 617 ARG cc_start: 0.8620 (mtt180) cc_final: 0.7903 (mtm180) REVERT: C 621 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8182 (tm-30) REVERT: C 622 ILE cc_start: 0.9064 (pt) cc_final: 0.8788 (mp) REVERT: C 626 MET cc_start: 0.8370 (mtm) cc_final: 0.7782 (mtm) REVERT: C 648 GLU cc_start: 0.9066 (pp20) cc_final: 0.8623 (pm20) REVERT: C 654 GLU cc_start: 0.8822 (tp30) cc_final: 0.8410 (tp30) REVERT: D 1 GLU cc_start: 0.6671 (pm20) cc_final: 0.6222 (pm20) REVERT: D 82 MET cc_start: 0.8439 (mmm) cc_final: 0.8197 (mmm) REVERT: D 82 LEU cc_start: 0.8697 (mt) cc_final: 0.8432 (tp) REVERT: D 102 TYR cc_start: 0.9414 (m-80) cc_final: 0.8925 (m-80) REVERT: E 35 TRP cc_start: 0.8262 (m-90) cc_final: 0.8052 (m-90) REVERT: E 37 GLN cc_start: 0.7912 (pp30) cc_final: 0.7344 (pp30) REVERT: E 45 LYS cc_start: 0.8846 (tptp) cc_final: 0.8421 (ttpp) REVERT: E 72 THR cc_start: 0.7023 (t) cc_final: 0.6556 (t) REVERT: F 573 ILE cc_start: 0.9265 (pt) cc_final: 0.9059 (pt) REVERT: F 577 GLN cc_start: 0.9149 (mt0) cc_final: 0.8847 (mt0) REVERT: F 584 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8755 (tm-30) REVERT: F 624 ASP cc_start: 0.8916 (m-30) cc_final: 0.8648 (m-30) REVERT: F 648 GLU cc_start: 0.9063 (pp20) cc_final: 0.8555 (pm20) REVERT: F 654 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8684 (tp30) REVERT: G 98 ASN cc_start: 0.8719 (t0) cc_final: 0.7910 (t0) REVERT: G 102 GLU cc_start: 0.9324 (mp0) cc_final: 0.9104 (mp0) REVERT: G 114 GLN cc_start: 0.9405 (tm-30) cc_final: 0.9118 (tm-30) REVERT: G 302 ASN cc_start: 0.8345 (t0) cc_final: 0.7828 (t0) REVERT: G 321 ASP cc_start: 0.8665 (t70) cc_final: 0.8216 (t70) REVERT: G 325 ASP cc_start: 0.8898 (p0) cc_final: 0.8368 (p0) REVERT: G 426 MET cc_start: 0.8743 (ptm) cc_final: 0.8200 (ptm) REVERT: G 434 MET cc_start: 0.8087 (tmm) cc_final: 0.7658 (tmm) REVERT: H 1 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8384 (pm20) REVERT: H 58 TYR cc_start: 0.5876 (p90) cc_final: 0.5154 (p90) REVERT: H 67 PHE cc_start: 0.8787 (p90) cc_final: 0.8194 (p90) REVERT: I 98 ASN cc_start: 0.8481 (t0) cc_final: 0.7502 (t0) REVERT: I 102 GLU cc_start: 0.9267 (mp0) cc_final: 0.8819 (mp0) REVERT: I 114 GLN cc_start: 0.9398 (tm-30) cc_final: 0.9071 (tm-30) REVERT: I 230 ASP cc_start: 0.8542 (t0) cc_final: 0.8332 (t0) REVERT: I 252 LYS cc_start: 0.9352 (mtmm) cc_final: 0.8940 (mtpp) REVERT: I 340 GLU cc_start: 0.9184 (tp30) cc_final: 0.8980 (tp30) REVERT: I 425 ASN cc_start: 0.9353 (p0) cc_final: 0.9068 (p0) REVERT: I 475 MET cc_start: 0.6192 (tmm) cc_final: 0.5941 (tmm) REVERT: I 482 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8572 (mm-30) REVERT: J 1 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8091 (pm20) REVERT: J 27 PHE cc_start: 0.8230 (m-10) cc_final: 0.7892 (m-10) REVERT: J 29 PHE cc_start: 0.8694 (t80) cc_final: 0.8439 (t80) REVERT: J 36 TRP cc_start: 0.8325 (m100) cc_final: 0.7835 (m100) REVERT: J 44 ARG cc_start: 0.5758 (mmt-90) cc_final: 0.5285 (mmt-90) REVERT: J 82 LEU cc_start: 0.8469 (mt) cc_final: 0.7983 (tp) REVERT: J 85 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8085 (tm-30) REVERT: J 91 TYR cc_start: 0.8657 (m-80) cc_final: 0.8174 (m-80) REVERT: J 102 TYR cc_start: 0.9290 (m-80) cc_final: 0.8549 (m-80) REVERT: K 23 CYS cc_start: 0.8881 (t) cc_final: 0.8194 (t) REVERT: K 37 GLN cc_start: 0.8043 (pp30) cc_final: 0.7135 (pp30) REVERT: K 38 GLN cc_start: 0.8673 (pt0) cc_final: 0.7563 (tt0) REVERT: K 45 LYS cc_start: 0.9011 (tptm) cc_final: 0.8795 (ttpt) REVERT: L 37 GLN cc_start: 0.8066 (pp30) cc_final: 0.7279 (pp30) REVERT: L 38 GLN cc_start: 0.8673 (pt0) cc_final: 0.7552 (tt0) REVERT: L 97 THR cc_start: 0.9052 (m) cc_final: 0.8815 (p) outliers start: 11 outliers final: 7 residues processed: 580 average time/residue: 0.1273 time to fit residues: 115.6170 Evaluate side-chains 445 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 438 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [153, 226, 28, 23, 107, 94, 26, 222, 90, 122, 155] chunk 153 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 122 optimal weight: 0.0170 chunk 155 optimal weight: 8.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS B 66 HIS B 85 HIS B 258 GLN C 650 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN F 650 GLN G 66 HIS G 440 GLN I 66 HIS K 6 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.090139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.072655 restraints weight = 63492.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075049 restraints weight = 33600.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076680 restraints weight = 21712.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.077813 restraints weight = 15863.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078589 restraints weight = 12614.442| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20698 Z= 0.137 Angle : 0.879 17.575 28237 Z= 0.414 Chirality : 0.052 0.323 3337 Planarity : 0.005 0.084 3463 Dihedral : 7.185 40.536 2607 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.32 % Favored : 85.47 % Rotamer: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.30 % 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: -4.10 (0.15), residues: 2388 helix: -1.90 (0.24), residues: 357 sheet: -1.28 (0.27), residues: 402 loop : -3.58 (0.12), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 71 TYR 0.027 0.002 TYR I 217 PHE 0.032 0.001 PHE D 27 TRP 0.025 0.001 TRP G 427 HIS 0.014 0.002 HIS E 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (20587) covalent geometry : angle 0.83574 / 0.40 (27934) SS BOND : bond 0.00666 / 0.46 ( 27) SS BOND : angle 1.64912 / 1.09 ( 54) hydrogen bonds : bond 0.04812 / 3.17 ( 414) hydrogen bonds : angle 5.91692 / 4.16 ( 1026) Misc. bond : bond 0.00021 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00838 / 0.40 ( 2) link_ALPHA1-3 : angle 2.42166 / 1.32 ( 6) link_ALPHA1-6 : bond 0.00451 / 0.22 ( 2) link_ALPHA1-6 : angle 1.44422 / 0.76 ( 6) link_BETA1-4 : bond 0.00677 / 0.40 ( 28) link_BETA1-4 : angle 2.22179 / 1.48 ( 84) link_NAG-ASN : bond 0.00637 / 0.40 ( 51) link_NAG-ASN : angle 3.32832 / 2.21 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 593 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8833 (mmt) cc_final: 0.8585 (mmm) REVERT: A 584 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8401 (tm-30) REVERT: A 621 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 626 MET cc_start: 0.8202 (mtm) cc_final: 0.7894 (mtp) REVERT: A 648 GLU cc_start: 0.9019 (pp20) cc_final: 0.8676 (pp20) REVERT: B 98 ASN cc_start: 0.8504 (t0) cc_final: 0.7271 (t0) REVERT: B 99 ASN cc_start: 0.9253 (m-40) cc_final: 0.8986 (m-40) REVERT: B 114 GLN cc_start: 0.9265 (tm-30) cc_final: 0.9060 (tm-30) REVERT: B 321 ASP cc_start: 0.8897 (t70) cc_final: 0.8420 (t0) REVERT: B 427 TRP cc_start: 0.8567 (m100) cc_final: 0.8180 (m100) REVERT: B 452 LEU cc_start: 0.9403 (pt) cc_final: 0.8851 (pp) REVERT: C 584 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 617 ARG cc_start: 0.8461 (mtt180) cc_final: 0.8013 (mtm180) REVERT: C 621 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 622 ILE cc_start: 0.9157 (pt) cc_final: 0.8919 (pt) REVERT: C 626 MET cc_start: 0.8005 (mtm) cc_final: 0.7440 (mtm) REVERT: C 648 GLU cc_start: 0.9092 (pp20) cc_final: 0.8678 (pm20) REVERT: D 39 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8231 (mm-40) REVERT: D 44 ARG cc_start: 0.6887 (mmt180) cc_final: 0.6616 (mmt-90) REVERT: D 91 TYR cc_start: 0.7772 (m-80) cc_final: 0.7214 (m-10) REVERT: E 27 TYR cc_start: 0.7549 (p90) cc_final: 0.7330 (p90) REVERT: E 37 GLN cc_start: 0.7946 (pp30) cc_final: 0.7382 (pp30) REVERT: E 45 LYS cc_start: 0.8831 (tptp) cc_final: 0.8394 (ttpp) REVERT: E 72 THR cc_start: 0.6954 (t) cc_final: 0.6322 (t) REVERT: E 78 VAL cc_start: 0.8389 (m) cc_final: 0.8114 (p) REVERT: E 82 ASP cc_start: 0.8942 (m-30) cc_final: 0.8573 (m-30) REVERT: F 536 THR cc_start: 0.9156 (m) cc_final: 0.8764 (p) REVERT: F 544 LEU cc_start: 0.9305 (tp) cc_final: 0.9046 (mt) REVERT: F 584 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8648 (tm-30) REVERT: F 621 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7114 (tm-30) REVERT: F 626 MET cc_start: 0.7620 (mtt) cc_final: 0.7190 (mpp) REVERT: F 648 GLU cc_start: 0.8986 (pp20) cc_final: 0.8568 (pm20) REVERT: G 92 GLU cc_start: 0.5282 (pt0) cc_final: 0.5081 (pt0) REVERT: G 98 ASN cc_start: 0.8496 (t0) cc_final: 0.7514 (t0) REVERT: G 102 GLU cc_start: 0.9280 (mp0) cc_final: 0.8829 (mp0) REVERT: G 114 GLN cc_start: 0.9423 (tm-30) cc_final: 0.9111 (tm-30) REVERT: G 211 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8891 (tm-30) REVERT: G 252 LYS cc_start: 0.9381 (mmtp) cc_final: 0.9127 (mmmm) REVERT: G 302 ASN cc_start: 0.8147 (t0) cc_final: 0.7671 (t0) REVERT: G 321 ASP cc_start: 0.8600 (t70) cc_final: 0.8268 (t70) REVERT: G 325 ASP cc_start: 0.8894 (p0) cc_final: 0.8330 (p0) REVERT: G 434 MET cc_start: 0.8143 (tmm) cc_final: 0.7694 (tmm) REVERT: H 1 GLU cc_start: 0.8760 (tm-30) cc_final: 0.7928 (pm20) REVERT: H 27 PHE cc_start: 0.8181 (m-10) cc_final: 0.7759 (m-80) REVERT: H 67 PHE cc_start: 0.8715 (p90) cc_final: 0.8006 (p90) REVERT: I 98 ASN cc_start: 0.8035 (t0) cc_final: 0.7435 (t0) REVERT: I 102 GLU cc_start: 0.9270 (mp0) cc_final: 0.8743 (mp0) REVERT: I 114 GLN cc_start: 0.9367 (tm-30) cc_final: 0.9061 (tm-30) REVERT: I 252 LYS cc_start: 0.9315 (mtmm) cc_final: 0.8929 (mtpp) REVERT: I 321 ASP cc_start: 0.8583 (t70) cc_final: 0.8380 (t70) REVERT: I 425 ASN cc_start: 0.9343 (p0) cc_final: 0.9020 (p0) REVERT: I 483 LEU cc_start: 0.9489 (pp) cc_final: 0.9205 (mt) REVERT: J 1 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8278 (pm20) REVERT: J 36 TRP cc_start: 0.8238 (m100) cc_final: 0.7970 (m100) REVERT: J 57 THR cc_start: 0.7401 (m) cc_final: 0.6895 (m) REVERT: J 67 PHE cc_start: 0.8225 (p90) cc_final: 0.7658 (p90) REVERT: J 82 LEU cc_start: 0.8668 (mt) cc_final: 0.8080 (tp) REVERT: J 85 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8076 (tm-30) REVERT: J 102 TYR cc_start: 0.9229 (m-80) cc_final: 0.8571 (m-80) REVERT: K 37 GLN cc_start: 0.8060 (pp30) cc_final: 0.7271 (pp30) REVERT: K 38 GLN cc_start: 0.8602 (pt0) cc_final: 0.7398 (tt0) REVERT: K 45 LYS cc_start: 0.9169 (tptm) cc_final: 0.8728 (ttpt) REVERT: K 81 GLU cc_start: 0.8988 (pp20) cc_final: 0.8731 (pp20) REVERT: K 82 ASP cc_start: 0.9158 (m-30) cc_final: 0.8292 (m-30) REVERT: L 37 GLN cc_start: 0.7890 (pp30) cc_final: 0.7177 (pp30) REVERT: L 38 GLN cc_start: 0.8565 (pt0) cc_final: 0.7813 (tt0) REVERT: L 78 VAL cc_start: 0.8336 (m) cc_final: 0.7928 (m) REVERT: L 82 ASP cc_start: 0.8852 (m-30) cc_final: 0.7685 (m-30) outliers start: 2 outliers final: 1 residues processed: 595 average time/residue: 0.1296 time to fit residues: 120.6431 Evaluate side-chains 432 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [43, 234, 134, 87, 78, 123, 161, 110, 42, 205, 12] chunk 43 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS B 258 GLN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN G 66 HIS G 440 GLN ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 440 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.088127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.070439 restraints weight = 69080.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.072678 restraints weight = 37400.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.074204 restraints weight = 24813.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.075248 restraints weight = 18583.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.075982 restraints weight = 15127.429| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20698 Z= 0.168 Angle : 0.874 16.394 28237 Z= 0.416 Chirality : 0.052 0.385 3337 Planarity : 0.005 0.084 3463 Dihedral : 7.042 44.238 2607 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.20 % Favored : 84.63 % Rotamer: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.30 % 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: -3.81 (0.15), residues: 2388 helix: -1.45 (0.26), residues: 357 sheet: -1.05 (0.27), residues: 396 loop : -3.44 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 44 TYR 0.020 0.002 TYR J 91 PHE 0.015 0.001 PHE E 98 TRP 0.032 0.002 TRP L 35 HIS 0.013 0.002 HIS E 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (20587) covalent geometry : angle 0.83787 / 0.41 (27934) SS BOND : bond 0.00384 / 0.21 ( 27) SS BOND : angle 1.72694 / 1.18 ( 54) hydrogen bonds : bond 0.04273 / 2.80 ( 414) hydrogen bonds : angle 5.66001 / 4.01 ( 1026) Misc. bond : bond 0.00006 / 0.00 ( 1) link_ALPHA1-3 : bond 0.00727 / 0.35 ( 2) link_ALPHA1-3 : angle 2.40362 / 1.31 ( 6) link_ALPHA1-6 : bond 0.00430 / 0.21 ( 2) link_ALPHA1-6 : angle 1.40060 / 0.73 ( 6) link_BETA1-4 : bond 0.00573 / 0.33 ( 28) link_BETA1-4 : angle 2.13430 / 1.41 ( 84) link_NAG-ASN : bond 0.00596 / 0.36 ( 51) link_NAG-ASN : angle 3.00608 / 2.00 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 528 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8907 (mmt) cc_final: 0.8676 (mmm) REVERT: A 536 THR cc_start: 0.9166 (m) cc_final: 0.8879 (p) REVERT: A 584 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8537 (tm-30) REVERT: A 621 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 626 MET cc_start: 0.7833 (mtm) cc_final: 0.7498 (mtp) REVERT: A 648 GLU cc_start: 0.9139 (pp20) cc_final: 0.8846 (pp20) REVERT: B 98 ASN cc_start: 0.8186 (t0) cc_final: 0.7182 (t0) REVERT: B 102 GLU cc_start: 0.9302 (mp0) cc_final: 0.9078 (mp0) REVERT: B 114 GLN cc_start: 0.9363 (tm-30) cc_final: 0.9133 (tm-30) REVERT: B 427 TRP cc_start: 0.8763 (m100) cc_final: 0.8309 (m100) REVERT: B 452 LEU cc_start: 0.9444 (pt) cc_final: 0.9119 (pp) REVERT: C 530 MET cc_start: 0.8704 (mmp) cc_final: 0.8273 (mmp) REVERT: C 584 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8455 (tm-30) REVERT: C 617 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8130 (mtm180) REVERT: C 621 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 626 MET cc_start: 0.7998 (mtm) cc_final: 0.7665 (mtm) REVERT: C 648 GLU cc_start: 0.9133 (pp20) cc_final: 0.8698 (pm20) REVERT: D 39 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8314 (mm110) REVERT: D 67 PHE cc_start: 0.8748 (p90) cc_final: 0.7994 (p90) REVERT: D 91 TYR cc_start: 0.7681 (m-80) cc_final: 0.6912 (m-10) REVERT: D 102 TYR cc_start: 0.9353 (m-80) cc_final: 0.8986 (m-80) REVERT: E 33 MET cc_start: 0.7470 (ptt) cc_final: 0.5962 (mtm) REVERT: E 37 GLN cc_start: 0.7743 (pp30) cc_final: 0.7465 (pp30) REVERT: E 45 LYS cc_start: 0.8830 (tptp) cc_final: 0.8420 (ttpp) REVERT: E 72 THR cc_start: 0.7290 (t) cc_final: 0.6785 (t) REVERT: E 78 VAL cc_start: 0.8311 (m) cc_final: 0.8010 (p) REVERT: E 82 ASP cc_start: 0.8908 (m-30) cc_final: 0.8410 (m-30) REVERT: F 536 THR cc_start: 0.9130 (m) cc_final: 0.8789 (p) REVERT: F 584 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8636 (tm-30) REVERT: F 621 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8552 (tm-30) REVERT: F 648 GLU cc_start: 0.9091 (pp20) cc_final: 0.8692 (pm20) REVERT: G 92 GLU cc_start: 0.5260 (pt0) cc_final: 0.4982 (pt0) REVERT: G 98 ASN cc_start: 0.8089 (t0) cc_final: 0.7354 (t0) REVERT: G 102 GLU cc_start: 0.9349 (mp0) cc_final: 0.8983 (mp0) REVERT: G 114 GLN cc_start: 0.9412 (tm-30) cc_final: 0.9175 (tm-30) REVERT: G 150 MET cc_start: 0.9242 (tmm) cc_final: 0.8984 (tmm) REVERT: G 252 LYS cc_start: 0.9479 (mmtp) cc_final: 0.9077 (mmmm) REVERT: G 302 ASN cc_start: 0.8180 (t0) cc_final: 0.7895 (t0) REVERT: G 426 MET cc_start: 0.8617 (ptm) cc_final: 0.8343 (ptm) REVERT: G 434 MET cc_start: 0.8338 (tmm) cc_final: 0.7800 (tmm) REVERT: H 1 GLU cc_start: 0.8969 (tm-30) cc_final: 0.7943 (pm20) REVERT: H 27 PHE cc_start: 0.8327 (m-10) cc_final: 0.7818 (m-80) REVERT: H 57 THR cc_start: 0.7741 (m) cc_final: 0.7162 (t) REVERT: H 67 PHE cc_start: 0.8413 (p90) cc_final: 0.7730 (p90) REVERT: I 59 LYS cc_start: 0.8032 (tptp) cc_final: 0.7821 (tptp) REVERT: I 98 ASN cc_start: 0.8283 (t0) cc_final: 0.7743 (t0) REVERT: I 102 GLU cc_start: 0.9313 (mp0) cc_final: 0.8590 (mp0) REVERT: I 104 MET cc_start: 0.9575 (mmt) cc_final: 0.9170 (mmm) REVERT: I 114 GLN cc_start: 0.9434 (tm-30) cc_final: 0.9119 (tm-30) REVERT: I 205 CYS cc_start: 0.7293 (t) cc_final: 0.7068 (t) REVERT: I 252 LYS cc_start: 0.9360 (mtmm) cc_final: 0.8946 (mtpp) REVERT: I 425 ASN cc_start: 0.9325 (p0) cc_final: 0.9037 (p0) REVERT: J 1 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8263 (pm20) REVERT: J 36 TRP cc_start: 0.8574 (m100) cc_final: 0.8153 (m100) REVERT: J 39 GLN cc_start: 0.8363 (tp40) cc_final: 0.8062 (tm-30) REVERT: J 57 THR cc_start: 0.7494 (m) cc_final: 0.6981 (m) REVERT: J 67 PHE cc_start: 0.8658 (p90) cc_final: 0.7996 (p90) REVERT: J 87 THR cc_start: 0.8740 (p) cc_final: 0.8251 (p) REVERT: K 27 TYR cc_start: 0.7565 (p90) cc_final: 0.7239 (p90) REVERT: K 33 MET cc_start: 0.7262 (ptt) cc_final: 0.6083 (mtm) REVERT: K 37 GLN cc_start: 0.8130 (pp30) cc_final: 0.7571 (pp30) REVERT: K 45 LYS cc_start: 0.9184 (tptm) cc_final: 0.8818 (ttpt) REVERT: K 78 VAL cc_start: 0.8400 (m) cc_final: 0.8198 (p) REVERT: K 81 GLU cc_start: 0.9368 (pp20) cc_final: 0.8990 (pp20) REVERT: L 37 GLN cc_start: 0.8040 (pp30) cc_final: 0.7335 (pp30) REVERT: L 38 GLN cc_start: 0.8888 (pt0) cc_final: 0.7721 (tt0) REVERT: L 81 GLU cc_start: 0.9057 (pp20) cc_final: 0.8785 (pp20) outliers start: 1 outliers final: 0 residues processed: 528 average time/residue: 0.1280 time to fit residues: 106.3666 Evaluate side-chains 418 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [48, 163, 74, 194, 17, 231, 157, 113, 105, 82, 137] chunk 48 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 231 optimal weight: 0.5980 chunk 157 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 203 GLN B 276 ASN B 330 HIS ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN F 585 HIS F 616 ASN G 66 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 GLN ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN I 66 HIS ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.067331 restraints weight = 70431.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.069505 restraints weight = 38419.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.070972 restraints weight = 25584.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.071981 restraints weight = 19279.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.072685 restraints weight = 15767.596| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20698 Z= 0.231 Angle : 0.913 14.886 28237 Z= 0.437 Chirality : 0.053 0.383 3337 Planarity : 0.005 0.079 3463 Dihedral : 7.095 39.491 2607 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.54 % Favored : 83.38 % Rotamer: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.30 % 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: -3.88 (0.15), residues: 2388 helix: -1.36 (0.25), residues: 366 sheet: -1.14 (0.28), residues: 366 loop : -3.49 (0.13), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 178 TYR 0.027 0.002 TYR I 217 PHE 0.023 0.002 PHE J 29 TRP 0.041 0.002 TRP L 35 HIS 0.012 0.002 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (20587) covalent geometry : angle 0.88086 / 0.43 (27934) SS BOND : bond 0.00475 / 0.32 ( 27) SS BOND : angle 1.80005 / 1.23 ( 54) hydrogen bonds : bond 0.04476 / 2.90 ( 414) hydrogen bonds : angle 5.76267 / 4.08 ( 1026) Misc. bond : bond 0.00017 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00695 / 0.34 ( 2) link_ALPHA1-3 : angle 2.40563 / 1.29 ( 6) link_ALPHA1-6 : bond 0.00368 / 0.18 ( 2) link_ALPHA1-6 : angle 1.38132 / 0.72 ( 6) link_BETA1-4 : bond 0.00556 / 0.33 ( 28) link_BETA1-4 : angle 2.14533 / 1.40 ( 84) link_NAG-ASN : bond 0.00573 / 0.37 ( 51) link_NAG-ASN : angle 2.83526 / 1.90 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 488 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 THR cc_start: 0.9184 (m) cc_final: 0.8951 (p) REVERT: A 584 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8621 (tm-30) REVERT: A 621 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 626 MET cc_start: 0.7760 (mtm) cc_final: 0.7516 (mtm) REVERT: A 635 ILE cc_start: 0.9387 (mp) cc_final: 0.9160 (mp) REVERT: A 648 GLU cc_start: 0.9214 (pp20) cc_final: 0.8884 (pp20) REVERT: A 654 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8690 (tp30) REVERT: B 98 ASN cc_start: 0.8241 (t0) cc_final: 0.7588 (t0) REVERT: B 104 MET cc_start: 0.9242 (ttp) cc_final: 0.9011 (ttp) REVERT: B 114 GLN cc_start: 0.9421 (tm-30) cc_final: 0.9187 (tm-30) REVERT: B 203 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8745 (pp30) REVERT: B 211 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8731 (tm-30) REVERT: B 427 TRP cc_start: 0.8877 (m100) cc_final: 0.8559 (m100) REVERT: C 530 MET cc_start: 0.8938 (mmp) cc_final: 0.8624 (mmp) REVERT: C 584 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8513 (tm-30) REVERT: C 617 ARG cc_start: 0.8611 (mtt180) cc_final: 0.8228 (mtm180) REVERT: C 621 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7980 (tm-30) REVERT: C 622 ILE cc_start: 0.9240 (pt) cc_final: 0.8909 (pt) REVERT: C 626 MET cc_start: 0.8045 (mtm) cc_final: 0.7336 (mtm) REVERT: C 648 GLU cc_start: 0.9169 (pp20) cc_final: 0.8728 (pm20) REVERT: D 39 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8313 (mm110) REVERT: D 44 ARG cc_start: 0.5908 (mmt-90) cc_final: 0.5587 (mmt-90) REVERT: D 67 PHE cc_start: 0.8670 (p90) cc_final: 0.8341 (p90) REVERT: D 102 TYR cc_start: 0.9396 (m-80) cc_final: 0.9045 (m-80) REVERT: E 33 MET cc_start: 0.7757 (ptt) cc_final: 0.6632 (mtm) REVERT: E 37 GLN cc_start: 0.7794 (pp30) cc_final: 0.7337 (pp30) REVERT: E 45 LYS cc_start: 0.9036 (tptp) cc_final: 0.8503 (ttpp) REVERT: E 78 VAL cc_start: 0.8323 (m) cc_final: 0.8047 (p) REVERT: E 82 ASP cc_start: 0.9042 (m-30) cc_final: 0.8548 (m-30) REVERT: E 97 THR cc_start: 0.9010 (p) cc_final: 0.8680 (t) REVERT: F 536 THR cc_start: 0.9144 (m) cc_final: 0.8836 (p) REVERT: F 584 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8734 (tm-30) REVERT: F 621 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 624 ASP cc_start: 0.9008 (m-30) cc_final: 0.8784 (m-30) REVERT: F 648 GLU cc_start: 0.9126 (pp20) cc_final: 0.8701 (pm20) REVERT: G 104 MET cc_start: 0.9175 (ttp) cc_final: 0.8762 (mtp) REVERT: G 114 GLN cc_start: 0.9486 (tm-30) cc_final: 0.9197 (tm-30) REVERT: G 150 MET cc_start: 0.9277 (tmm) cc_final: 0.8991 (tmm) REVERT: G 252 LYS cc_start: 0.9535 (mmtp) cc_final: 0.9125 (mmmm) REVERT: G 434 MET cc_start: 0.8410 (tmm) cc_final: 0.8008 (tmm) REVERT: G 475 MET cc_start: 0.7743 (tmm) cc_final: 0.7343 (tmm) REVERT: H 29 PHE cc_start: 0.8723 (t80) cc_final: 0.8372 (t80) REVERT: H 67 PHE cc_start: 0.8367 (p90) cc_final: 0.8071 (p90) REVERT: H 78 LEU cc_start: 0.8669 (pp) cc_final: 0.8429 (pp) REVERT: I 59 LYS cc_start: 0.8072 (tptp) cc_final: 0.7844 (tptp) REVERT: I 98 ASN cc_start: 0.8091 (t0) cc_final: 0.7661 (t0) REVERT: I 102 GLU cc_start: 0.9309 (mp0) cc_final: 0.8691 (mp0) REVERT: I 104 MET cc_start: 0.9528 (mmm) cc_final: 0.8892 (tpp) REVERT: I 114 GLN cc_start: 0.9453 (tm-30) cc_final: 0.9147 (tm-30) REVERT: I 217 TYR cc_start: 0.7490 (m-10) cc_final: 0.7128 (m-10) REVERT: I 252 LYS cc_start: 0.9375 (mtmm) cc_final: 0.9028 (mmmm) REVERT: I 425 ASN cc_start: 0.9363 (p0) cc_final: 0.9068 (p0) REVERT: J 36 TRP cc_start: 0.8431 (m100) cc_final: 0.7939 (m100) REVERT: J 39 GLN cc_start: 0.8248 (tp40) cc_final: 0.7951 (tm-30) REVERT: J 57 THR cc_start: 0.7691 (m) cc_final: 0.6891 (m) REVERT: J 67 PHE cc_start: 0.8770 (p90) cc_final: 0.7989 (p90) REVERT: J 87 THR cc_start: 0.8700 (p) cc_final: 0.8222 (p) REVERT: K 27 TYR cc_start: 0.7798 (p90) cc_final: 0.7488 (p90) REVERT: K 35 TRP cc_start: 0.8627 (m-10) cc_final: 0.8256 (m-10) REVERT: K 37 GLN cc_start: 0.8042 (pp30) cc_final: 0.7619 (pp30) REVERT: K 38 GLN cc_start: 0.8152 (pt0) cc_final: 0.7950 (pt0) REVERT: K 45 LYS cc_start: 0.9168 (tptm) cc_final: 0.8812 (ttpp) REVERT: L 37 GLN cc_start: 0.8065 (pp30) cc_final: 0.7305 (pp30) REVERT: L 38 GLN cc_start: 0.8831 (pt0) cc_final: 0.7677 (tt0) REVERT: L 82 ASP cc_start: 0.8870 (m-30) cc_final: 0.8002 (m-30) outliers start: 3 outliers final: 0 residues processed: 490 average time/residue: 0.1232 time to fit residues: 95.1861 Evaluate side-chains 394 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [29, 9, 110, 223, 156, 73, 93, 120, 69, 35, 166] chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 93 optimal weight: 0.0470 chunk 120 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS F 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.069476 restraints weight = 69145.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.071687 restraints weight = 37826.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.073173 restraints weight = 25208.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.074227 restraints weight = 19016.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074957 restraints weight = 15536.866| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20698 Z= 0.153 Angle : 0.874 14.556 28237 Z= 0.413 Chirality : 0.052 0.345 3337 Planarity : 0.005 0.074 3463 Dihedral : 6.907 37.267 2607 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.66 % Favored : 85.26 % Rotamer: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.30 % 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: -3.77 (0.15), residues: 2388 helix: -1.25 (0.25), residues: 369 sheet: -1.31 (0.26), residues: 399 loop : -3.38 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 61 TYR 0.026 0.002 TYR J 58 PHE 0.030 0.001 PHE J 29 TRP 0.029 0.002 TRP L 35 HIS 0.010 0.002 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (20587) covalent geometry : angle 0.83893 / 0.41 (27934) SS BOND : bond 0.00588 / 0.42 ( 27) SS BOND : angle 1.50519 / 0.99 ( 54) hydrogen bonds : bond 0.04042 / 2.66 ( 414) hydrogen bonds : angle 5.57822 / 3.95 ( 1026) Misc. bond : bond 0.00130 / 0.07 ( 1) link_ALPHA1-3 : bond 0.00673 / 0.32 ( 2) link_ALPHA1-3 : angle 2.29609 / 1.23 ( 6) link_ALPHA1-6 : bond 0.00448 / 0.22 ( 2) link_ALPHA1-6 : angle 1.39280 / 0.72 ( 6) link_BETA1-4 : bond 0.00624 / 0.35 ( 28) link_BETA1-4 : angle 2.02679 / 1.34 ( 84) link_NAG-ASN : bond 0.00868 / 0.47 ( 51) link_NAG-ASN : angle 3.00820 / 1.99 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 519 time to evaluate : 0.735 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: A 536 THR cc_start: 0.9159 (m) cc_final: 0.8902 (p) REVERT: A 584 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8553 (tm-30) REVERT: A 621 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8112 (tm-30) REVERT: A 648 GLU cc_start: 0.9207 (pp20) cc_final: 0.8855 (pp20) REVERT: A 654 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8612 (tp30) REVERT: B 98 ASN cc_start: 0.7851 (t0) cc_final: 0.6946 (t0) REVERT: B 102 GLU cc_start: 0.9293 (mp0) cc_final: 0.9092 (mp0) REVERT: B 114 GLN cc_start: 0.9404 (tm-30) cc_final: 0.9113 (tm-30) REVERT: B 211 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8747 (tm-30) REVERT: B 252 LYS cc_start: 0.9413 (mtmm) cc_final: 0.9109 (mmmm) REVERT: B 427 TRP cc_start: 0.8821 (m100) cc_final: 0.8484 (m100) REVERT: C 530 MET cc_start: 0.8881 (mmp) cc_final: 0.8315 (mmp) REVERT: C 584 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8489 (tm-30) REVERT: C 617 ARG cc_start: 0.8494 (mtt180) cc_final: 0.8279 (mtm180) REVERT: C 621 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 622 ILE cc_start: 0.9215 (pt) cc_final: 0.8867 (pt) REVERT: C 626 MET cc_start: 0.8036 (mtm) cc_final: 0.7222 (mtm) REVERT: C 645 LEU cc_start: 0.9416 (tp) cc_final: 0.8861 (tp) REVERT: C 648 GLU cc_start: 0.9147 (pp20) cc_final: 0.8705 (pm20) REVERT: D 36 TRP cc_start: 0.8639 (m100) cc_final: 0.8305 (m-10) REVERT: D 67 PHE cc_start: 0.8741 (p90) cc_final: 0.8190 (p90) REVERT: D 82 MET cc_start: 0.7949 (mmp) cc_final: 0.7609 (mmp) REVERT: D 102 TYR cc_start: 0.9351 (m-80) cc_final: 0.9059 (m-80) REVERT: E 33 MET cc_start: 0.7649 (ptt) cc_final: 0.7296 (ptp) REVERT: E 37 GLN cc_start: 0.7681 (pp30) cc_final: 0.7361 (pp30) REVERT: E 45 LYS cc_start: 0.8915 (tptp) cc_final: 0.8497 (ttpp) REVERT: E 82 ASP cc_start: 0.9101 (m-30) cc_final: 0.8819 (m-30) REVERT: F 536 THR cc_start: 0.9205 (m) cc_final: 0.8860 (p) REVERT: F 584 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8707 (tm-30) REVERT: F 621 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8439 (tm-30) REVERT: F 624 ASP cc_start: 0.8972 (m-30) cc_final: 0.8771 (m-30) REVERT: F 648 GLU cc_start: 0.9143 (pp20) cc_final: 0.8704 (pm20) REVERT: G 98 ASN cc_start: 0.8526 (t0) cc_final: 0.8124 (t0) REVERT: G 104 MET cc_start: 0.9193 (ttp) cc_final: 0.8895 (mtp) REVERT: G 114 GLN cc_start: 0.9464 (tm-30) cc_final: 0.9170 (tm-30) REVERT: G 150 MET cc_start: 0.9256 (tmm) cc_final: 0.8945 (tmm) REVERT: G 161 MET cc_start: 0.9240 (tpp) cc_final: 0.9035 (tpp) REVERT: G 252 LYS cc_start: 0.9482 (mmtp) cc_final: 0.9100 (mmmm) REVERT: G 302 ASN cc_start: 0.8307 (t0) cc_final: 0.8081 (t0) REVERT: G 434 MET cc_start: 0.8362 (tmm) cc_final: 0.7918 (tmm) REVERT: G 475 MET cc_start: 0.7529 (tmm) cc_final: 0.7241 (tmm) REVERT: H 47 TRP cc_start: 0.6183 (m-90) cc_final: 0.5902 (m-90) REVERT: H 67 PHE cc_start: 0.8686 (p90) cc_final: 0.8029 (p90) REVERT: H 72 ASP cc_start: 0.8829 (t70) cc_final: 0.8474 (t0) REVERT: I 59 LYS cc_start: 0.8003 (tptp) cc_final: 0.7782 (tptp) REVERT: I 98 ASN cc_start: 0.8249 (t0) cc_final: 0.7889 (t0) REVERT: I 102 GLU cc_start: 0.9318 (mp0) cc_final: 0.9040 (mp0) REVERT: I 104 MET cc_start: 0.9615 (mmm) cc_final: 0.9204 (mmm) REVERT: I 114 GLN cc_start: 0.9437 (tm-30) cc_final: 0.9117 (tm-30) REVERT: I 217 TYR cc_start: 0.7472 (m-10) cc_final: 0.7203 (m-10) REVERT: I 252 LYS cc_start: 0.9362 (mtmm) cc_final: 0.8986 (mtpp) REVERT: I 425 ASN cc_start: 0.9320 (p0) cc_final: 0.9046 (p0) REVERT: I 434 MET cc_start: 0.9273 (tpp) cc_final: 0.8674 (tpp) REVERT: J 22 CYS cc_start: 0.8889 (t) cc_final: 0.8630 (t) REVERT: J 36 TRP cc_start: 0.8439 (m100) cc_final: 0.7953 (m100) REVERT: J 39 GLN cc_start: 0.8357 (tp40) cc_final: 0.7973 (tm-30) REVERT: J 57 THR cc_start: 0.7665 (m) cc_final: 0.6892 (m) REVERT: J 67 PHE cc_start: 0.8567 (p90) cc_final: 0.7782 (p90) REVERT: K 27 TYR cc_start: 0.7966 (p90) cc_final: 0.7585 (p90) REVERT: K 45 LYS cc_start: 0.9151 (tptm) cc_final: 0.8813 (ttpp) REVERT: L 72 THR cc_start: 0.8454 (p) cc_final: 0.8191 (p) outliers start: 2 outliers final: 0 residues processed: 519 average time/residue: 0.1245 time to fit residues: 102.3154 Evaluate side-chains 404 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [133, 83, 121, 203, 75, 15, 211, 113, 91, 58, 140] chunk 133 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS A 650 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN F 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN K 53 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.068180 restraints weight = 69705.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.070344 restraints weight = 38170.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.071824 restraints weight = 25530.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072848 restraints weight = 19283.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073554 restraints weight = 15787.882| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20698 Z= 0.188 Angle : 0.886 14.586 28237 Z= 0.423 Chirality : 0.053 0.327 3337 Planarity : 0.005 0.069 3463 Dihedral : 6.937 36.546 2607 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.83 % Favored : 84.00 % Rotamer: Outliers : 0.14 % Allowed : 1.99 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.30 % 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: -3.76 (0.15), residues: 2388 helix: -1.08 (0.25), residues: 369 sheet: -1.32 (0.27), residues: 375 loop : -3.39 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 44 TYR 0.031 0.002 TYR J 58 PHE 0.029 0.002 PHE J 29 TRP 0.045 0.002 TRP L 35 HIS 0.010 0.002 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (20587) covalent geometry : angle 0.85241 / 0.42 (27934) SS BOND : bond 0.00531 / 0.37 ( 27) SS BOND : angle 1.90943 / 1.24 ( 54) hydrogen bonds : bond 0.04026 / 2.67 ( 414) hydrogen bonds : angle 5.55737 / 3.94 ( 1026) Misc. bond : bond 0.00108 / 0.06 ( 1) link_ALPHA1-3 : bond 0.00641 / 0.31 ( 2) link_ALPHA1-3 : angle 2.36885 / 1.27 ( 6) link_ALPHA1-6 : bond 0.00406 / 0.21 ( 2) link_ALPHA1-6 : angle 1.36771 / 0.71 ( 6) link_BETA1-4 : bond 0.00543 / 0.30 ( 28) link_BETA1-4 : angle 2.05659 / 1.35 ( 84) link_NAG-ASN : bond 0.00636 / 0.37 ( 51) link_NAG-ASN : angle 2.88005 / 1.94 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 496 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: symmetry clash REVERT: A 536 THR cc_start: 0.9160 (m) cc_final: 0.8935 (p) REVERT: A 584 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8599 (tm-30) REVERT: A 626 MET cc_start: 0.7891 (mtm) cc_final: 0.7594 (mtt) REVERT: A 648 GLU cc_start: 0.9188 (pp20) cc_final: 0.8888 (pp20) REVERT: A 654 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8589 (tp30) REVERT: B 98 ASN cc_start: 0.8336 (t0) cc_final: 0.7276 (t0) REVERT: B 104 MET cc_start: 0.9131 (ttp) cc_final: 0.8797 (ttp) REVERT: B 114 GLN cc_start: 0.9429 (tm-30) cc_final: 0.9159 (tm-30) REVERT: B 252 LYS cc_start: 0.9406 (mtmm) cc_final: 0.9135 (mmmm) REVERT: B 427 TRP cc_start: 0.8914 (m100) cc_final: 0.8669 (m100) REVERT: C 530 MET cc_start: 0.9024 (mmp) cc_final: 0.8818 (mmp) REVERT: C 584 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8480 (tm-30) REVERT: C 621 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8007 (tm-30) REVERT: C 622 ILE cc_start: 0.9276 (pt) cc_final: 0.8877 (pt) REVERT: C 626 MET cc_start: 0.8048 (mtm) cc_final: 0.7413 (mtm) REVERT: C 645 LEU cc_start: 0.9446 (tp) cc_final: 0.8924 (tp) REVERT: C 648 GLU cc_start: 0.9185 (pp20) cc_final: 0.8712 (pm20) REVERT: C 657 GLU cc_start: 0.9206 (mp0) cc_final: 0.8619 (mp0) REVERT: D 36 TRP cc_start: 0.8738 (m100) cc_final: 0.8204 (m-10) REVERT: D 44 ARG cc_start: 0.5961 (mmt-90) cc_final: 0.5534 (mmt-90) REVERT: D 50 THR cc_start: 0.8917 (t) cc_final: 0.8701 (t) REVERT: D 67 PHE cc_start: 0.8684 (p90) cc_final: 0.8144 (p90) REVERT: D 82 MET cc_start: 0.7976 (mmp) cc_final: 0.7754 (mmp) REVERT: E 23 CYS cc_start: 0.8674 (t) cc_final: 0.8462 (t) REVERT: E 33 MET cc_start: 0.7439 (ptt) cc_final: 0.6946 (ptp) REVERT: E 37 GLN cc_start: 0.7662 (pp30) cc_final: 0.7390 (pp30) REVERT: E 45 LYS cc_start: 0.9072 (tptp) cc_final: 0.8553 (ttpp) REVERT: E 78 VAL cc_start: 0.8240 (m) cc_final: 0.7957 (p) REVERT: E 82 ASP cc_start: 0.8968 (m-30) cc_final: 0.8350 (m-30) REVERT: E 97 THR cc_start: 0.8905 (p) cc_final: 0.8627 (t) REVERT: F 536 THR cc_start: 0.9166 (m) cc_final: 0.8836 (p) REVERT: F 584 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8728 (tm-30) REVERT: F 621 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8491 (tm-30) REVERT: F 624 ASP cc_start: 0.8958 (m-30) cc_final: 0.8742 (m-30) REVERT: F 648 GLU cc_start: 0.9147 (pp20) cc_final: 0.8644 (pm20) REVERT: G 98 ASN cc_start: 0.8416 (t0) cc_final: 0.8017 (t0) REVERT: G 102 GLU cc_start: 0.9213 (mp0) cc_final: 0.8989 (mp0) REVERT: G 114 GLN cc_start: 0.9470 (tm-30) cc_final: 0.9187 (tm-30) REVERT: G 150 MET cc_start: 0.9253 (tmm) cc_final: 0.8851 (tmm) REVERT: G 161 MET cc_start: 0.9184 (tpp) cc_final: 0.8970 (tpp) REVERT: G 434 MET cc_start: 0.8248 (tmm) cc_final: 0.7794 (tmm) REVERT: G 475 MET cc_start: 0.7728 (tmm) cc_final: 0.7476 (tmm) REVERT: H 39 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8240 (mm-40) REVERT: H 47 TRP cc_start: 0.6334 (m-90) cc_final: 0.6043 (m-90) REVERT: H 67 PHE cc_start: 0.8716 (p90) cc_final: 0.8037 (p90) REVERT: H 72 ASP cc_start: 0.8865 (t70) cc_final: 0.8597 (t0) REVERT: I 59 LYS cc_start: 0.8023 (tptp) cc_final: 0.7788 (tptp) REVERT: I 102 GLU cc_start: 0.9324 (mp0) cc_final: 0.9004 (mp0) REVERT: I 104 MET cc_start: 0.9541 (mmm) cc_final: 0.8883 (mmt) REVERT: I 114 GLN cc_start: 0.9490 (tm-30) cc_final: 0.9163 (tm-30) REVERT: I 217 TYR cc_start: 0.7486 (m-10) cc_final: 0.6594 (m-10) REVERT: I 252 LYS cc_start: 0.9376 (mtmm) cc_final: 0.9024 (mmmm) REVERT: I 425 ASN cc_start: 0.9314 (p0) cc_final: 0.9048 (p0) REVERT: I 434 MET cc_start: 0.9198 (tpp) cc_final: 0.8670 (tpp) REVERT: I 475 MET cc_start: 0.8206 (tpt) cc_final: 0.7973 (tpp) REVERT: J 36 TRP cc_start: 0.8441 (m100) cc_final: 0.7977 (m100) REVERT: J 57 THR cc_start: 0.7706 (m) cc_final: 0.6932 (m) REVERT: J 67 PHE cc_start: 0.8560 (p90) cc_final: 0.7923 (p90) REVERT: K 27 TYR cc_start: 0.7602 (p90) cc_final: 0.7318 (p90) REVERT: K 33 MET cc_start: 0.7305 (pmm) cc_final: 0.6827 (pmm) REVERT: K 45 LYS cc_start: 0.9160 (tptm) cc_final: 0.8833 (ttpp) REVERT: K 72 THR cc_start: 0.8593 (p) cc_final: 0.8346 (p) REVERT: K 82 ASP cc_start: 0.9176 (m-30) cc_final: 0.8093 (m-30) outliers start: 3 outliers final: 0 residues processed: 496 average time/residue: 0.1220 time to fit residues: 96.2297 Evaluate side-chains 393 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [177, 150, 200, 181, 97, 124, 171, 148, 34, 186, 178] chunk 177 optimal weight: 9.9990 chunk 150 optimal weight: 0.0470 chunk 200 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 171 optimal weight: 0.0870 chunk 148 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS B 66 HIS B 203 GLN B 352 HIS B 432 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN F 585 HIS F 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.069899 restraints weight = 68910.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.072100 restraints weight = 37745.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.073625 restraints weight = 25229.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.074667 restraints weight = 18988.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.075389 restraints weight = 15516.990| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20698 Z= 0.143 Angle : 0.860 14.661 28237 Z= 0.409 Chirality : 0.052 0.298 3337 Planarity : 0.005 0.065 3463 Dihedral : 6.753 35.153 2607 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.45 % Favored : 85.43 % Rotamer: Outliers : 0.28 % Allowed : 1.70 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.26 % 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: -3.65 (0.15), residues: 2388 helix: -0.95 (0.26), residues: 369 sheet: -1.31 (0.27), residues: 369 loop : -3.31 (0.13), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 44 TYR 0.031 0.002 TYR J 58 PHE 0.031 0.001 PHE J 29 TRP 0.054 0.002 TRP K 35 HIS 0.009 0.002 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (20587) covalent geometry : angle 0.82665 / 0.40 (27934) SS BOND : bond 0.00482 / 0.32 ( 27) SS BOND : angle 1.75061 / 1.16 ( 54) hydrogen bonds : bond 0.03856 / 2.56 ( 414) hydrogen bonds : angle 5.41339 / 3.85 ( 1026) Misc. bond : bond 0.00056 / 0.03 ( 1) link_ALPHA1-3 : bond 0.00653 / 0.31 ( 2) link_ALPHA1-3 : angle 2.23082 / 1.19 ( 6) link_ALPHA1-6 : bond 0.00465 / 0.23 ( 2) link_ALPHA1-6 : angle 1.39028 / 0.72 ( 6) link_BETA1-4 : bond 0.00563 / 0.31 ( 28) link_BETA1-4 : angle 1.93642 / 1.28 ( 84) link_NAG-ASN : bond 0.00663 / 0.38 ( 51) link_NAG-ASN : angle 2.88554 / 1.95 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 522 time to evaluate : 0.675 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 584 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8575 (tm-30) REVERT: A 621 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8253 (tm-30) REVERT: A 647 GLU cc_start: 0.8952 (pp20) cc_final: 0.8734 (pp20) REVERT: A 648 GLU cc_start: 0.9096 (pp20) cc_final: 0.8707 (pp20) REVERT: A 654 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8325 (pt0) REVERT: A 657 GLU cc_start: 0.9023 (mp0) cc_final: 0.8347 (mp0) REVERT: A 658 GLN cc_start: 0.9259 (tt0) cc_final: 0.8719 (tm-30) REVERT: B 98 ASN cc_start: 0.8313 (t0) cc_final: 0.6933 (t0) REVERT: B 102 GLU cc_start: 0.9362 (mp0) cc_final: 0.8672 (pm20) REVERT: B 104 MET cc_start: 0.9114 (ttp) cc_final: 0.8802 (ttp) REVERT: B 114 GLN cc_start: 0.9410 (tm-30) cc_final: 0.9117 (tm-30) REVERT: B 195 ASN cc_start: 0.8405 (p0) cc_final: 0.8192 (m-40) REVERT: B 203 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8652 (pp30) REVERT: B 211 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8769 (tm-30) REVERT: B 217 TYR cc_start: 0.7527 (m-10) cc_final: 0.6916 (m-10) REVERT: B 252 LYS cc_start: 0.9383 (mtmm) cc_final: 0.9125 (mmmm) REVERT: C 584 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8443 (tm-30) REVERT: C 617 ARG cc_start: 0.8462 (mtt180) cc_final: 0.8246 (mtm180) REVERT: C 621 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 622 ILE cc_start: 0.9254 (pt) cc_final: 0.8863 (pt) REVERT: C 626 MET cc_start: 0.8014 (mtm) cc_final: 0.7210 (mtm) REVERT: C 645 LEU cc_start: 0.9411 (tp) cc_final: 0.8931 (tp) REVERT: C 648 GLU cc_start: 0.9154 (pp20) cc_final: 0.8684 (pm20) REVERT: C 657 GLU cc_start: 0.9211 (mp0) cc_final: 0.8522 (mp0) REVERT: D 22 CYS cc_start: 0.8945 (t) cc_final: 0.8573 (t) REVERT: D 36 TRP cc_start: 0.8585 (m100) cc_final: 0.8187 (m-10) REVERT: D 50 THR cc_start: 0.8798 (t) cc_final: 0.8574 (t) REVERT: D 67 PHE cc_start: 0.8601 (p90) cc_final: 0.7955 (p90) REVERT: D 102 TYR cc_start: 0.9310 (m-80) cc_final: 0.9086 (m-80) REVERT: E 45 LYS cc_start: 0.9004 (tptp) cc_final: 0.8659 (ttpp) REVERT: E 78 VAL cc_start: 0.8093 (m) cc_final: 0.7729 (p) REVERT: E 82 ASP cc_start: 0.8904 (m-30) cc_final: 0.8393 (m-30) REVERT: F 573 ILE cc_start: 0.9182 (pt) cc_final: 0.8802 (pt) REVERT: F 577 GLN cc_start: 0.9140 (mt0) cc_final: 0.8879 (mt0) REVERT: F 584 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8708 (tm-30) REVERT: F 621 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8309 (tm-30) REVERT: F 624 ASP cc_start: 0.8936 (m-30) cc_final: 0.8730 (m-30) REVERT: F 640 GLN cc_start: 0.9482 (mm110) cc_final: 0.9060 (mm-40) REVERT: F 648 GLU cc_start: 0.9089 (pp20) cc_final: 0.8606 (pm20) REVERT: F 658 GLN cc_start: 0.9263 (tp40) cc_final: 0.8801 (tm-30) REVERT: G 98 ASN cc_start: 0.8441 (t0) cc_final: 0.7753 (t0) REVERT: G 102 GLU cc_start: 0.9258 (mp0) cc_final: 0.8993 (mp0) REVERT: G 114 GLN cc_start: 0.9435 (tm-30) cc_final: 0.9147 (tm-30) REVERT: G 150 MET cc_start: 0.9200 (tmm) cc_final: 0.8696 (tmm) REVERT: G 302 ASN cc_start: 0.8181 (t0) cc_final: 0.7895 (t0) REVERT: G 434 MET cc_start: 0.8193 (tmm) cc_final: 0.7706 (tmm) REVERT: H 39 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8183 (mm-40) REVERT: H 67 PHE cc_start: 0.8564 (p90) cc_final: 0.7718 (p90) REVERT: H 72 ASP cc_start: 0.8881 (t70) cc_final: 0.8630 (t0) REVERT: I 98 ASN cc_start: 0.8289 (t0) cc_final: 0.7969 (t0) REVERT: I 102 GLU cc_start: 0.9407 (mp0) cc_final: 0.9071 (mp0) REVERT: I 104 MET cc_start: 0.9549 (mmm) cc_final: 0.8852 (mmt) REVERT: I 114 GLN cc_start: 0.9468 (tm-30) cc_final: 0.9134 (tm-30) REVERT: I 217 TYR cc_start: 0.7440 (m-10) cc_final: 0.6942 (m-10) REVERT: I 252 LYS cc_start: 0.9329 (mtmm) cc_final: 0.9021 (mmmm) REVERT: I 425 ASN cc_start: 0.9294 (p0) cc_final: 0.9037 (p0) REVERT: I 434 MET cc_start: 0.9179 (tpp) cc_final: 0.8457 (tpp) REVERT: I 475 MET cc_start: 0.8162 (tpt) cc_final: 0.7720 (tpp) REVERT: J 22 CYS cc_start: 0.8802 (t) cc_final: 0.8585 (t) REVERT: J 36 TRP cc_start: 0.8367 (m100) cc_final: 0.7947 (m100) REVERT: J 39 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7867 (mm-40) REVERT: J 57 THR cc_start: 0.7590 (m) cc_final: 0.6755 (m) REVERT: J 67 PHE cc_start: 0.8506 (p90) cc_final: 0.7696 (p90) REVERT: K 27 TYR cc_start: 0.7342 (p90) cc_final: 0.7141 (p90) REVERT: K 33 MET cc_start: 0.7290 (pmm) cc_final: 0.6865 (pmm) REVERT: K 45 LYS cc_start: 0.9064 (tptm) cc_final: 0.8832 (ttpp) REVERT: K 72 THR cc_start: 0.8328 (p) cc_final: 0.7966 (p) REVERT: K 82 ASP cc_start: 0.8885 (m-30) cc_final: 0.8280 (m-30) REVERT: K 103 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8311 (mtmm) REVERT: L 78 VAL cc_start: 0.8184 (m) cc_final: 0.7910 (p) REVERT: L 82 ASP cc_start: 0.9083 (m-30) cc_final: 0.8865 (m-30) outliers start: 6 outliers final: 0 residues processed: 524 average time/residue: 0.1233 time to fit residues: 102.8635 Evaluate side-chains 424 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 423 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [90, 118, 190, 175, 101, 21, 97, 163, 126, 55, 177] chunk 90 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 101 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 163 optimal weight: 0.0670 chunk 126 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS A 658 GLN C 585 HIS ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN F 585 HIS F 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.071420 restraints weight = 67586.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.073686 restraints weight = 36893.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.075239 restraints weight = 24525.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.076314 restraints weight = 18386.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.076928 restraints weight = 14975.527| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20698 Z= 0.138 Angle : 0.870 14.739 28237 Z= 0.413 Chirality : 0.054 0.645 3337 Planarity : 0.005 0.062 3463 Dihedral : 6.710 35.281 2607 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.28 % Favored : 85.64 % Rotamer: Outliers : 0.14 % Allowed : 0.90 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.26 % 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: -3.55 (0.15), residues: 2388 helix: -0.61 (0.27), residues: 348 sheet: -1.21 (0.27), residues: 384 loop : -3.30 (0.13), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 44 TYR 0.031 0.002 TYR J 58 PHE 0.035 0.001 PHE H 29 TRP 0.062 0.002 TRP K 35 HIS 0.010 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (20587) covalent geometry : angle 0.83682 / 0.41 (27934) SS BOND : bond 0.00534 / 0.38 ( 27) SS BOND : angle 1.81691 / 1.18 ( 54) hydrogen bonds : bond 0.03686 / 2.45 ( 414) hydrogen bonds : angle 5.31523 / 3.79 ( 1026) Misc. bond : bond 0.00099 / 0.05 ( 1) link_ALPHA1-3 : bond 0.00628 / 0.30 ( 2) link_ALPHA1-3 : angle 2.24818 / 1.21 ( 6) link_ALPHA1-6 : bond 0.00481 / 0.24 ( 2) link_ALPHA1-6 : angle 1.38053 / 0.71 ( 6) link_BETA1-4 : bond 0.00583 / 0.32 ( 28) link_BETA1-4 : angle 1.87219 / 1.24 ( 84) link_NAG-ASN : bond 0.00789 / 0.44 ( 51) link_NAG-ASN : angle 2.90767 / 2.04 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 540 time to evaluate : 0.741 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 577 GLN cc_start: 0.9100 (mt0) cc_final: 0.8709 (mt0) REVERT: A 584 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8535 (tm-30) REVERT: A 652 GLN cc_start: 0.8759 (mp-120) cc_final: 0.8275 (mp10) REVERT: A 658 GLN cc_start: 0.9281 (tt0) cc_final: 0.8803 (tm-30) REVERT: B 98 ASN cc_start: 0.8257 (t0) cc_final: 0.6960 (t0) REVERT: B 102 GLU cc_start: 0.9346 (mp0) cc_final: 0.9003 (mp0) REVERT: B 104 MET cc_start: 0.9071 (ttp) cc_final: 0.8738 (ttp) REVERT: B 114 GLN cc_start: 0.9416 (tm-30) cc_final: 0.9125 (tm-30) REVERT: B 121 LYS cc_start: 0.9258 (ttmt) cc_final: 0.9054 (ttpp) REVERT: B 211 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8712 (tm-30) REVERT: B 217 TYR cc_start: 0.7255 (m-10) cc_final: 0.6680 (m-10) REVERT: B 252 LYS cc_start: 0.9360 (mtmm) cc_final: 0.9100 (mmmm) REVERT: C 573 ILE cc_start: 0.9087 (pt) cc_final: 0.8782 (pt) REVERT: C 577 GLN cc_start: 0.9116 (mt0) cc_final: 0.8833 (mt0) REVERT: C 584 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8486 (tm-30) REVERT: C 621 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 622 ILE cc_start: 0.9254 (pt) cc_final: 0.8801 (pt) REVERT: C 626 MET cc_start: 0.8007 (mtm) cc_final: 0.7179 (mtm) REVERT: C 645 LEU cc_start: 0.9403 (tp) cc_final: 0.8923 (tp) REVERT: C 648 GLU cc_start: 0.9143 (pp20) cc_final: 0.8678 (pm20) REVERT: C 657 GLU cc_start: 0.9205 (mp0) cc_final: 0.8453 (mp0) REVERT: C 658 GLN cc_start: 0.9111 (tp40) cc_final: 0.8850 (tm-30) REVERT: D 22 CYS cc_start: 0.8916 (t) cc_final: 0.8541 (t) REVERT: D 36 TRP cc_start: 0.8667 (m100) cc_final: 0.8235 (m-10) REVERT: D 39 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8175 (mm-40) REVERT: D 50 THR cc_start: 0.8848 (t) cc_final: 0.8640 (t) REVERT: D 57 THR cc_start: 0.7832 (m) cc_final: 0.7607 (m) REVERT: D 67 PHE cc_start: 0.8527 (p90) cc_final: 0.7808 (p90) REVERT: D 102 TYR cc_start: 0.9322 (m-80) cc_final: 0.9089 (m-80) REVERT: E 33 MET cc_start: 0.6349 (pmm) cc_final: 0.6030 (pmm) REVERT: E 37 GLN cc_start: 0.7422 (pp30) cc_final: 0.7167 (pp30) REVERT: E 38 GLN cc_start: 0.8773 (pt0) cc_final: 0.8570 (pt0) REVERT: E 45 LYS cc_start: 0.8971 (tptp) cc_final: 0.8651 (ttpp) REVERT: E 82 ASP cc_start: 0.8907 (m-30) cc_final: 0.8647 (m-30) REVERT: E 87 TYR cc_start: 0.8221 (m-80) cc_final: 0.7954 (m-80) REVERT: F 535 MET cc_start: 0.9126 (mmt) cc_final: 0.8854 (mmt) REVERT: F 573 ILE cc_start: 0.9172 (pt) cc_final: 0.8771 (pt) REVERT: F 584 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8699 (tm-30) REVERT: F 621 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8197 (tm-30) REVERT: F 624 ASP cc_start: 0.8965 (m-30) cc_final: 0.8759 (m-30) REVERT: F 640 GLN cc_start: 0.9477 (mm110) cc_final: 0.9032 (mm-40) REVERT: F 645 LEU cc_start: 0.9289 (tp) cc_final: 0.8952 (tp) REVERT: F 648 GLU cc_start: 0.9079 (pp20) cc_final: 0.8767 (pp20) REVERT: F 658 GLN cc_start: 0.9188 (tp40) cc_final: 0.8641 (tm-30) REVERT: G 98 ASN cc_start: 0.8592 (t0) cc_final: 0.8011 (t0) REVERT: G 114 GLN cc_start: 0.9394 (tm-30) cc_final: 0.9098 (tm-30) REVERT: G 150 MET cc_start: 0.9141 (tmm) cc_final: 0.8669 (tmm) REVERT: G 434 MET cc_start: 0.8162 (tmm) cc_final: 0.7685 (tmm) REVERT: H 13 LYS cc_start: 0.8938 (tppt) cc_final: 0.8619 (tppt) REVERT: H 39 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8137 (mm-40) REVERT: H 67 PHE cc_start: 0.8565 (p90) cc_final: 0.7755 (p90) REVERT: H 72 ASP cc_start: 0.8829 (t70) cc_final: 0.8629 (t0) REVERT: I 98 ASN cc_start: 0.8182 (t0) cc_final: 0.7929 (t0) REVERT: I 102 GLU cc_start: 0.9413 (mp0) cc_final: 0.9114 (mp0) REVERT: I 104 MET cc_start: 0.9516 (mmm) cc_final: 0.8872 (mmt) REVERT: I 114 GLN cc_start: 0.9409 (tm-30) cc_final: 0.9072 (tm-30) REVERT: I 180 ASP cc_start: 0.8772 (m-30) cc_final: 0.8562 (m-30) REVERT: I 217 TYR cc_start: 0.7431 (m-10) cc_final: 0.6742 (m-10) REVERT: I 252 LYS cc_start: 0.9319 (mtmm) cc_final: 0.9028 (mmmm) REVERT: I 425 ASN cc_start: 0.9347 (p0) cc_final: 0.9106 (p0) REVERT: I 434 MET cc_start: 0.9154 (tpp) cc_final: 0.8451 (tpp) REVERT: I 475 MET cc_start: 0.8242 (tpt) cc_final: 0.7674 (tpp) REVERT: J 22 CYS cc_start: 0.8802 (t) cc_final: 0.8441 (t) REVERT: J 36 TRP cc_start: 0.8185 (m100) cc_final: 0.7775 (m100) REVERT: J 57 THR cc_start: 0.7483 (m) cc_final: 0.6545 (m) REVERT: J 67 PHE cc_start: 0.8459 (p90) cc_final: 0.7658 (p90) REVERT: K 22 SER cc_start: 0.8705 (p) cc_final: 0.8502 (t) REVERT: K 33 MET cc_start: 0.7244 (pmm) cc_final: 0.6997 (pmm) REVERT: K 37 GLN cc_start: 0.7361 (pp30) cc_final: 0.6855 (pp30) REVERT: K 72 THR cc_start: 0.8009 (p) cc_final: 0.7655 (p) REVERT: K 73 LEU cc_start: 0.8044 (mp) cc_final: 0.7606 (mt) REVERT: K 103 LYS cc_start: 0.8608 (mmmm) cc_final: 0.8263 (mtmm) REVERT: L 33 MET cc_start: 0.6469 (pmm) cc_final: 0.6068 (pmm) REVERT: L 78 VAL cc_start: 0.8210 (m) cc_final: 0.7959 (p) REVERT: L 81 GLU cc_start: 0.9208 (pp20) cc_final: 0.8852 (pp20) outliers start: 3 outliers final: 0 residues processed: 540 average time/residue: 0.1217 time to fit residues: 105.1345 Evaluate side-chains 434 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [166, 100, 8, 151, 220, 94, 132, 0, 203, 82, 141] chunk 166 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 151 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS C 585 HIS C 650 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN F 616 ASN F 650 GLN G 66 HIS G 67 ASN G 330 HIS ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.068886 restraints weight = 69399.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.071061 restraints weight = 38070.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072569 restraints weight = 25545.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.073599 restraints weight = 19295.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.074317 restraints weight = 15835.413| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20698 Z= 0.183 Angle : 0.895 14.167 28237 Z= 0.427 Chirality : 0.055 0.681 3337 Planarity : 0.005 0.058 3463 Dihedral : 6.791 34.529 2607 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.87 % Favored : 84.05 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.30 % 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: -3.56 (0.15), residues: 2388 helix: -0.71 (0.27), residues: 354 sheet: -1.28 (0.28), residues: 369 loop : -3.26 (0.13), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 44 TYR 0.034 0.002 TYR H 58 PHE 0.033 0.002 PHE J 29 TRP 0.068 0.003 TRP K 35 HIS 0.008 0.002 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (20587) covalent geometry : angle 0.86129 / 0.42 (27934) SS BOND : bond 0.00522 / 0.38 ( 27) SS BOND : angle 1.82641 / 1.19 ( 54) hydrogen bonds : bond 0.03933 / 2.62 ( 414) hydrogen bonds : angle 5.41692 / 3.87 ( 1026) Misc. bond : bond 0.00003 / 0.00 ( 1) link_ALPHA1-3 : bond 0.00510 / 0.24 ( 2) link_ALPHA1-3 : angle 2.21227 / 1.19 ( 6) link_ALPHA1-6 : bond 0.00446 / 0.22 ( 2) link_ALPHA1-6 : angle 1.37280 / 0.71 ( 6) link_BETA1-4 : bond 0.00537 / 0.30 ( 28) link_BETA1-4 : angle 1.94525 / 1.27 ( 84) link_NAG-ASN : bond 0.00663 / 0.37 ( 51) link_NAG-ASN : angle 3.00540 / 2.06 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 513 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8504 (tm-30) REVERT: A 630 GLN cc_start: 0.9222 (mp10) cc_final: 0.8919 (mp10) REVERT: A 654 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8471 (tp30) REVERT: A 655 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8545 (mmmt) REVERT: A 658 GLN cc_start: 0.9300 (tt0) cc_final: 0.8967 (tm-30) REVERT: B 98 ASN cc_start: 0.8176 (t0) cc_final: 0.7295 (t0) REVERT: B 104 MET cc_start: 0.9055 (ttp) cc_final: 0.8739 (ttp) REVERT: B 114 GLN cc_start: 0.9418 (tm-30) cc_final: 0.9150 (tm-30) REVERT: B 217 TYR cc_start: 0.7356 (m-10) cc_final: 0.6760 (m-10) REVERT: B 252 LYS cc_start: 0.9363 (mtmm) cc_final: 0.9135 (mmmm) REVERT: B 427 TRP cc_start: 0.8828 (m100) cc_final: 0.8449 (m100) REVERT: C 540 GLN cc_start: 0.9051 (mp10) cc_final: 0.8729 (mp10) REVERT: C 573 ILE cc_start: 0.9132 (pt) cc_final: 0.8829 (pt) REVERT: C 577 GLN cc_start: 0.9142 (mt0) cc_final: 0.8873 (mt0) REVERT: C 584 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8439 (tm-30) REVERT: C 621 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7888 (tm-30) REVERT: C 622 ILE cc_start: 0.9231 (pt) cc_final: 0.8797 (pt) REVERT: C 626 MET cc_start: 0.8019 (mtm) cc_final: 0.7421 (mtm) REVERT: C 645 LEU cc_start: 0.9443 (tp) cc_final: 0.8937 (tp) REVERT: C 648 GLU cc_start: 0.9139 (pp20) cc_final: 0.8740 (pm20) REVERT: C 657 GLU cc_start: 0.9232 (mp0) cc_final: 0.8510 (mp0) REVERT: C 658 GLN cc_start: 0.9100 (tp40) cc_final: 0.8884 (tm-30) REVERT: D 22 CYS cc_start: 0.8880 (t) cc_final: 0.8440 (t) REVERT: D 39 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8242 (mm-40) REVERT: D 44 ARG cc_start: 0.5858 (mmt-90) cc_final: 0.4975 (mmt-90) REVERT: D 57 THR cc_start: 0.7891 (m) cc_final: 0.7617 (m) REVERT: D 67 PHE cc_start: 0.8679 (p90) cc_final: 0.7859 (p90) REVERT: D 71 ARG cc_start: 0.8284 (tmt-80) cc_final: 0.7705 (tmt-80) REVERT: D 85 GLU cc_start: 0.8519 (pp20) cc_final: 0.8142 (pp20) REVERT: D 102 TYR cc_start: 0.9282 (m-80) cc_final: 0.9020 (m-80) REVERT: E 33 MET cc_start: 0.6590 (pmm) cc_final: 0.6274 (pmm) REVERT: E 45 LYS cc_start: 0.9000 (tptp) cc_final: 0.8602 (ttpp) REVERT: E 78 VAL cc_start: 0.8114 (m) cc_final: 0.7773 (p) REVERT: E 82 ASP cc_start: 0.8853 (m-30) cc_final: 0.8449 (m-30) REVERT: F 540 GLN cc_start: 0.8914 (mp10) cc_final: 0.8692 (mp10) REVERT: F 573 ILE cc_start: 0.9154 (pt) cc_final: 0.8773 (pt) REVERT: F 577 GLN cc_start: 0.9138 (mt0) cc_final: 0.8749 (mt0) REVERT: F 584 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8708 (tm-30) REVERT: F 621 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8312 (tm-30) REVERT: F 624 ASP cc_start: 0.8911 (m-30) cc_final: 0.8628 (m-30) REVERT: F 634 GLU cc_start: 0.9231 (tm-30) cc_final: 0.9030 (tm-30) REVERT: F 648 GLU cc_start: 0.9093 (pp20) cc_final: 0.8702 (pm20) REVERT: F 655 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8652 (mppt) REVERT: F 656 ASN cc_start: 0.8777 (t0) cc_final: 0.8567 (t0) REVERT: F 658 GLN cc_start: 0.9107 (tp40) cc_final: 0.8749 (tm-30) REVERT: G 98 ASN cc_start: 0.8923 (t0) cc_final: 0.8446 (t0) REVERT: G 102 GLU cc_start: 0.9293 (mp0) cc_final: 0.9083 (mp0) REVERT: G 114 GLN cc_start: 0.9444 (tm-30) cc_final: 0.9146 (tm-30) REVERT: G 150 MET cc_start: 0.9063 (tmm) cc_final: 0.8825 (tmm) REVERT: G 302 ASN cc_start: 0.8114 (t0) cc_final: 0.7801 (t0) REVERT: G 434 MET cc_start: 0.8218 (tmm) cc_final: 0.7955 (tmm) REVERT: G 475 MET cc_start: 0.7237 (tmm) cc_final: 0.6116 (tpp) REVERT: H 13 LYS cc_start: 0.8915 (tppt) cc_final: 0.8670 (tppt) REVERT: H 39 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8156 (mm-40) REVERT: H 67 PHE cc_start: 0.8653 (p90) cc_final: 0.7769 (p90) REVERT: H 72 ASP cc_start: 0.8900 (t70) cc_final: 0.8663 (t0) REVERT: I 98 ASN cc_start: 0.8298 (t0) cc_final: 0.7903 (t0) REVERT: I 102 GLU cc_start: 0.9453 (mp0) cc_final: 0.8998 (mp0) REVERT: I 104 MET cc_start: 0.9410 (mmm) cc_final: 0.8711 (mmt) REVERT: I 114 GLN cc_start: 0.9494 (tm-30) cc_final: 0.9164 (tm-30) REVERT: I 180 ASP cc_start: 0.8778 (m-30) cc_final: 0.8574 (m-30) REVERT: I 217 TYR cc_start: 0.7458 (m-10) cc_final: 0.6846 (m-10) REVERT: I 252 LYS cc_start: 0.9381 (mtmm) cc_final: 0.9039 (mmmm) REVERT: I 425 ASN cc_start: 0.9302 (p0) cc_final: 0.9051 (p0) REVERT: I 434 MET cc_start: 0.9144 (tpp) cc_final: 0.8481 (tpp) REVERT: I 475 MET cc_start: 0.8063 (tpt) cc_final: 0.7447 (tpp) REVERT: J 22 CYS cc_start: 0.8853 (t) cc_final: 0.8503 (t) REVERT: J 36 TRP cc_start: 0.8405 (m100) cc_final: 0.7928 (m100) REVERT: J 39 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7774 (mm-40) REVERT: J 57 THR cc_start: 0.7596 (m) cc_final: 0.6730 (m) REVERT: J 67 PHE cc_start: 0.8504 (p90) cc_final: 0.7889 (p90) REVERT: K 21 ILE cc_start: 0.9144 (pt) cc_final: 0.8828 (pt) REVERT: K 33 MET cc_start: 0.7074 (pmm) cc_final: 0.6736 (pmm) REVERT: K 37 GLN cc_start: 0.7648 (pp30) cc_final: 0.7396 (pp30) REVERT: K 72 THR cc_start: 0.8073 (p) cc_final: 0.7829 (p) REVERT: K 103 LYS cc_start: 0.8673 (mmmm) cc_final: 0.8314 (mtmm) REVERT: L 33 MET cc_start: 0.6537 (pmm) cc_final: 0.6066 (pmm) REVERT: L 78 VAL cc_start: 0.8098 (m) cc_final: 0.7857 (p) REVERT: L 82 ASP cc_start: 0.9129 (m-30) cc_final: 0.8896 (m-30) outliers start: 3 outliers final: 0 residues processed: 513 average time/residue: 0.1225 time to fit residues: 99.5657 Evaluate side-chains 410 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [71, 92, 81, 221, 217, 224, 65, 199, 4, 103, 230] chunk 71 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 221 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 199 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 230 optimal weight: 0.0970 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN F 616 ASN I 66 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.071552 restraints weight = 68492.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.073817 restraints weight = 37579.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.075381 restraints weight = 25119.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076446 restraints weight = 18906.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.077188 restraints weight = 15446.597| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20698 Z= 0.142 Angle : 0.876 14.433 28237 Z= 0.419 Chirality : 0.054 0.585 3337 Planarity : 0.005 0.084 3463 Dihedral : 6.712 34.992 2607 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.74 % Favored : 86.18 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.30 % 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: -3.46 (0.15), residues: 2388 helix: -0.76 (0.27), residues: 354 sheet: -0.95 (0.30), residues: 339 loop : -3.20 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 44 TYR 0.035 0.002 TYR K 96 PHE 0.034 0.001 PHE H 29 TRP 0.059 0.002 TRP K 35 HIS 0.010 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (20587) covalent geometry : angle 0.84447 / 0.41 (27934) SS BOND : bond 0.00416 / 0.28 ( 27) SS BOND : angle 1.72104 / 1.10 ( 54) hydrogen bonds : bond 0.03849 / 2.61 ( 414) hydrogen bonds : angle 5.22034 / 3.76 ( 1026) Misc. bond : bond 0.00080 / 0.04 ( 1) link_ALPHA1-3 : bond 0.00774 / 0.37 ( 2) link_ALPHA1-3 : angle 2.19566 / 1.18 ( 6) link_ALPHA1-6 : bond 0.00470 / 0.24 ( 2) link_ALPHA1-6 : angle 1.39948 / 0.72 ( 6) link_BETA1-4 : bond 0.00580 / 0.32 ( 28) link_BETA1-4 : angle 1.83990 / 1.22 ( 84) link_NAG-ASN : bond 0.00722 / 0.41 ( 51) link_NAG-ASN : angle 2.85893 / 1.97 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3203.00 seconds wall clock time: 56 minutes 30.15 seconds (3390.15 seconds total)