Starting phenix.real_space_refine on Thu Sep 18 19:57:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d7i_46606/09_2025/9d7i_46606.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d7i_46606/09_2025/9d7i_46606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d7i_46606/09_2025/9d7i_46606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d7i_46606/09_2025/9d7i_46606.map" model { file = "/net/cci-nas-00/data/ceres_data/9d7i_46606/09_2025/9d7i_46606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d7i_46606/09_2025/9d7i_46606.cif" } resolution = 3.68 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= 0.026 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 123 5.16 5 C 12329 2.51 5 N 3275 2.21 5 O 3948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19675 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3373 Classifications: {'peptide': 429} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "B" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1008 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3447 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "D" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3447 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "F" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1447 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 175} Chain breaks: 5 Chain: "H" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1189 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1447 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 175} Chain breaks: 5 Chain: "J" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1189 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.97, per 1000 atoms: 0.25 Number of scatterers: 19675 At special positions: 0 Unit cell: (164.16, 128.52, 167.4, 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 123 16.00 O 3948 8.00 N 3275 7.00 C 12329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 247 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 385 " distance=2.05 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 418 " distance=2.09 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " 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 c 2 " - " BMA c 3 " " 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 g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 276 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 332 " " NAG A 607 " - " ASN A 355 " " NAG A 608 " - " ASN A 392 " " NAG A 609 " - " ASN A 448 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 301 " " NAG C 602 " - " ASN C 448 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 355 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 133 " " NAG C 607 " - " ASN C 137 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 137 " " NAG E 603 " - " ASN E 152 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 355 " " NAG E 608 " - " ASN E 392 " " NAG E 609 " - " ASN E 448 " " NAG F 702 " - " ASN F 637 " " NAG K 1 " - " ASN A 133 " " NAG L 1 " - " ASN A 148 " " NAG M 1 " - " ASN A 152 " " NAG N 1 " - " ASN A 197 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 363 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN C 363 " " NAG T 1 " - " ASN C 332 " " NAG U 1 " - " ASN C 295 " " NAG V 1 " - " ASN C 276 " " NAG W 1 " - " ASN C 152 " " NAG X 1 " - " ASN C 262 " " NAG Y 1 " - " ASN C 148 " " NAG Z 1 " - " ASN C 88 " " NAG a 1 " - " ASN E 88 " " NAG b 1 " - " ASN E 148 " " NAG c 1 " - " ASN E 262 " " NAG e 1 " - " ASN E 295 " " NAG f 1 " - " ASN E 332 " " NAG g 1 " - " ASN E 363 " " NAG h 1 " - " ASN E 386 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 873.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4414 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 48 sheets defined 15.6% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.786A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.696A pdb=" N TRP A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.921A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.981A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.924A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 537 through 543' Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.520A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 removed outlier: 3.582A pdb=" N GLN B 630 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP B 632 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.982A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.693A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.655A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.720A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 543 removed outlier: 4.206A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 removed outlier: 3.810A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 622 removed outlier: 3.651A pdb=" N GLU D 621 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 622 " --> pdb=" O LEU D 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 618 through 622' Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 654 removed outlier: 3.988A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.613A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 350 removed outlier: 3.763A pdb=" N TRP E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.924A pdb=" N THR E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 373' Processing helix chain 'E' and resid 474 through 479 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.592A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.583A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 634 removed outlier: 3.515A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 646 removed outlier: 4.131A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.017A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.738A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.663A pdb=" N GLU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.811A pdb=" N LYS J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.642A pdb=" N ASP J 86 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 83 through 87' Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 3.915A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 4.085A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 244 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.606A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.702A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.923A pdb=" N MET A 271 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 287 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASN A 332 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.923A pdb=" N MET A 271 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 287 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.741A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 361 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.568A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.932A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.406A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB8, first strand: chain 'C' and resid 166 through 169 Processing sheet with id=AB9, first strand: chain 'C' and resid 152 through 154 Processing sheet with id=AC1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.435A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 259 through 261 removed outlier: 10.087A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.143A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.087A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AC5, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AC6, first strand: chain 'E' and resid 46 through 47 removed outlier: 3.793A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.792A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 161 through 169 Processing sheet with id=AC9, first strand: chain 'E' and resid 259 through 261 removed outlier: 5.947A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 272 Processing sheet with id=AD2, first strand: chain 'E' and resid 307 through 312 removed outlier: 3.552A pdb=" N ILE E 307 " --> pdb=" O PHE E 317 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.432A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 383 through 385 Processing sheet with id=AD5, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD6, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.508A pdb=" N ASP G 85 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TRP G 35 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AD8, first strand: chain 'G' and resid 19 through 23 removed outlier: 3.527A pdb=" N ALA G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 114 through 118 removed outlier: 4.035A pdb=" N PHE G 118 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL G 133 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR G 172 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 145 through 149 removed outlier: 3.564A pdb=" N LYS G 204 " --> pdb=" O CYS G 193 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL G 195 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 202 " --> pdb=" O VAL G 195 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.549A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'I' and resid 9 through 13 removed outlier: 3.946A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLN I 37 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 9 through 13 removed outlier: 3.549A pdb=" N VAL I 90 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL I 97 " --> pdb=" O VAL I 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 19 through 23 removed outlier: 3.521A pdb=" N ALA I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.777A pdb=" N PHE I 118 " --> pdb=" O VAL I 133 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL I 133 " --> pdb=" O LEU I 178 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU I 178 " --> pdb=" O VAL I 133 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU I 135 " --> pdb=" O SER I 176 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER I 176 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER I 137 " --> pdb=" O ALA I 174 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA I 174 " --> pdb=" O SER I 137 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 144 through 149 removed outlier: 3.537A pdb=" N CYS I 193 " --> pdb=" O LYS I 204 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS I 204 " --> pdb=" O CYS I 193 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.529A pdb=" N GLN J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 11 through 13 removed outlier: 3.773A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER J 40 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU J 45 " --> pdb=" O SER J 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 169 through 170 565 hydrogen bonds defined for protein. 1509 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: 3.88 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6109 1.35 - 1.48: 5362 1.48 - 1.62: 8439 1.62 - 1.75: 0 1.75 - 1.88: 160 Bond restraints: 20070 Sorted by residual: bond pdb=" C ASP C 78 " pdb=" N PRO C 79 " ideal model delta sigma weight residual 1.332 1.438 -0.106 1.26e-02 6.30e+03 7.10e+01 bond pdb=" C ASP A 78 " pdb=" N PRO A 79 " ideal model delta sigma weight residual 1.334 1.417 -0.083 2.34e-02 1.83e+03 1.26e+01 bond pdb=" CA THR C 135 " pdb=" CB THR C 135 " ideal model delta sigma weight residual 1.523 1.563 -0.040 1.35e-02 5.49e+03 8.59e+00 bond pdb=" N ASN E 136 " pdb=" CA ASN E 136 " ideal model delta sigma weight residual 1.461 1.487 -0.026 9.70e-03 1.06e+04 7.42e+00 bond pdb=" C SER B 546 " pdb=" N GLY B 547 " ideal model delta sigma weight residual 1.333 1.360 -0.027 1.00e-02 1.00e+04 7.31e+00 ... (remaining 20065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 26577 3.09 - 6.17: 583 6.17 - 9.26: 87 9.26 - 12.34: 17 12.34 - 15.43: 17 Bond angle restraints: 27281 Sorted by residual: angle pdb=" N ILE F 635 " pdb=" CA ILE F 635 " pdb=" C ILE F 635 " ideal model delta sigma weight residual 113.10 106.50 6.60 9.70e-01 1.06e+00 4.63e+01 angle pdb=" O THR E 135 " pdb=" C THR E 135 " pdb=" N ASN E 136 " ideal model delta sigma weight residual 123.06 114.43 8.63 1.36e+00 5.41e-01 4.03e+01 angle pdb=" O THR C 135 " pdb=" C THR C 135 " pdb=" N ASN C 136 " ideal model delta sigma weight residual 123.40 116.58 6.82 1.13e+00 7.83e-01 3.65e+01 angle pdb=" C VAL E 496 " pdb=" N ALA E 497 " pdb=" CA ALA E 497 " ideal model delta sigma weight residual 121.80 136.41 -14.61 2.44e+00 1.68e-01 3.58e+01 angle pdb=" CA CYS E 418 " pdb=" CB CYS E 418 " pdb=" SG CYS E 418 " ideal model delta sigma weight residual 114.40 128.10 -13.70 2.30e+00 1.89e-01 3.55e+01 ... (remaining 27276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.73: 12328 22.73 - 45.46: 674 45.46 - 68.20: 110 68.20 - 90.93: 29 90.93 - 113.66: 4 Dihedral angle restraints: 13145 sinusoidal: 6320 harmonic: 6825 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 15.88 77.12 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" CB CYS E 331 " pdb=" SG CYS E 331 " pdb=" SG CYS E 418 " pdb=" CB CYS E 418 " ideal model delta sinusoidal sigma weight residual 93.00 20.62 72.38 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CB CYS E 385 " pdb=" SG CYS E 385 " pdb=" SG CYS E 418 " pdb=" CB CYS E 418 " ideal model delta sinusoidal sigma weight residual -86.00 -15.02 -70.98 1 1.00e+01 1.00e-02 6.47e+01 ... (remaining 13142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 3085 0.112 - 0.224: 242 0.224 - 0.336: 21 0.336 - 0.449: 5 0.449 - 0.561: 1 Chirality restraints: 3354 Sorted by residual: chirality pdb=" CB ILE C 176 " pdb=" CA ILE C 176 " pdb=" CG1 ILE C 176 " pdb=" CG2 ILE C 176 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" CB ILE E 453 " pdb=" CA ILE E 453 " pdb=" CG1 ILE E 453 " pdb=" CG2 ILE E 453 " both_signs ideal model delta sigma weight residual False 2.64 3.07 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C1 NAG A 609 " pdb=" ND2 ASN A 448 " pdb=" C2 NAG A 609 " pdb=" O5 NAG A 609 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 3351 not shown) Planarity restraints: 3392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 78 " 0.042 2.00e-02 2.50e+03 8.02e-02 6.43e+01 pdb=" C ASP A 78 " -0.139 2.00e-02 2.50e+03 pdb=" O ASP A 78 " 0.053 2.00e-02 2.50e+03 pdb=" N PRO A 79 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 78 " -0.040 2.00e-02 2.50e+03 7.75e-02 6.00e+01 pdb=" C ASP C 78 " 0.134 2.00e-02 2.50e+03 pdb=" O ASP C 78 " -0.052 2.00e-02 2.50e+03 pdb=" N PRO C 79 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 78 " -0.039 2.00e-02 2.50e+03 7.71e-02 5.95e+01 pdb=" C ASP E 78 " 0.133 2.00e-02 2.50e+03 pdb=" O ASP E 78 " -0.052 2.00e-02 2.50e+03 pdb=" N PRO E 79 " -0.043 2.00e-02 2.50e+03 ... (remaining 3389 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2032 2.76 - 3.29: 17433 3.29 - 3.83: 30920 3.83 - 4.36: 33034 4.36 - 4.90: 59523 Nonbonded interactions: 142942 Sorted by model distance: nonbonded pdb=" OG1 THR E 373 " pdb=" O CYS E 385 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR G 181 " pdb=" OE1 GLN G 184 " model vdw 2.265 3.040 nonbonded pdb=" O ASP F 632 " pdb=" OG SER F 636 " model vdw 2.280 3.040 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.286 3.040 nonbonded pdb=" OG SER G 63 " pdb=" OG1 THR G 74 " model vdw 2.314 3.040 ... (remaining 142937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 34 through 607) selection = (chain 'C' and (resid 34 through 135 or resid 144 through 397 or resid 412 throu \ gh 607)) selection = (chain 'E' and (resid 34 through 135 or resid 144 through 397 or resid 412 throu \ gh 607)) } ncs_group { reference = (chain 'B' and (resid 521 through 546 or resid 569 through 701)) selection = (chain 'D' and resid 521 through 701) selection = (chain 'F' and resid 521 through 701) } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'c' selection = chain 'd' selection = chain 'g' selection = chain 'h' } 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.010 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 20191 Z= 0.259 Angle : 1.202 20.641 27608 Z= 0.605 Chirality : 0.063 0.561 3354 Planarity : 0.008 0.083 3341 Dihedral : 13.522 113.660 8623 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.16), residues: 2300 helix: -0.75 (0.27), residues: 311 sheet: -0.91 (0.20), residues: 671 loop : -2.06 (0.15), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 76 TYR 0.036 0.002 TYR E 39 PHE 0.051 0.002 PHE C 53 TRP 0.068 0.003 TRP A 69 HIS 0.013 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00513 (20070) covalent geometry : angle 1.14919 (27281) SS BOND : bond 0.01253 ( 36) SS BOND : angle 4.18956 ( 72) hydrogen bonds : bond 0.23227 ( 548) hydrogen bonds : angle 8.23604 ( 1509) link_BETA1-4 : bond 0.00783 ( 34) link_BETA1-4 : angle 2.57598 ( 102) link_NAG-ASN : bond 0.00541 ( 51) link_NAG-ASN : angle 3.53706 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7915 (p0) cc_final: 0.7499 (p0) REVERT: A 207 LYS cc_start: 0.7401 (tmtt) cc_final: 0.7121 (tmtt) REVERT: A 265 LEU cc_start: 0.8575 (mp) cc_final: 0.8106 (tp) REVERT: A 294 ILE cc_start: 0.8432 (pt) cc_final: 0.8089 (mt) REVERT: D 601 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8777 (ttmm) REVERT: D 633 LYS cc_start: 0.8655 (mttt) cc_final: 0.8416 (mptt) REVERT: D 656 ASN cc_start: 0.8566 (m-40) cc_final: 0.8226 (m-40) REVERT: E 153 MET cc_start: 0.7880 (tpp) cc_final: 0.7322 (tpp) REVERT: E 170 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7789 (tpp-160) REVERT: E 213 ILE cc_start: 0.8858 (tp) cc_final: 0.8651 (tt) REVERT: E 364 SER cc_start: 0.8966 (t) cc_final: 0.8652 (p) REVERT: F 605 CYS cc_start: 0.8751 (p) cc_final: 0.8531 (p) REVERT: F 621 GLU cc_start: 0.8273 (pt0) cc_final: 0.7834 (tp30) REVERT: G 138 ASP cc_start: 0.8510 (t70) cc_final: 0.7883 (t70) REVERT: H 102 ASN cc_start: 0.8406 (m-40) cc_final: 0.8032 (t0) REVERT: I 53 LYS cc_start: 0.8996 (mttt) cc_final: 0.8657 (mttm) REVERT: I 110 LYS cc_start: 0.8509 (tmtt) cc_final: 0.7929 (tptt) REVERT: I 138 ASP cc_start: 0.7408 (m-30) cc_final: 0.6604 (p0) REVERT: J 166 PHE cc_start: 0.7757 (m-80) cc_final: 0.7438 (m-80) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1516 time to fit residues: 75.0844 Evaluate side-chains 250 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN C 188 ASN D 630 GLN E 67 ASN E 374 HIS F 653 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 170 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.124785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095195 restraints weight = 42358.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100211 restraints weight = 22358.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101436 restraints weight = 12954.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.101030 restraints weight = 10188.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101774 restraints weight = 11322.527| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20191 Z= 0.133 Angle : 0.732 12.489 27608 Z= 0.345 Chirality : 0.047 0.376 3354 Planarity : 0.005 0.051 3341 Dihedral : 8.920 110.730 4341 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 1.35 % Allowed : 7.40 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.17), residues: 2300 helix: 0.51 (0.30), residues: 313 sheet: -0.63 (0.20), residues: 696 loop : -1.86 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 61 TYR 0.016 0.001 TYR E 484 PHE 0.017 0.001 PHE E 53 TRP 0.021 0.001 TRP C 35 HIS 0.003 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00293 (20070) covalent geometry : angle 0.68025 (27281) SS BOND : bond 0.00574 ( 36) SS BOND : angle 2.34880 ( 72) hydrogen bonds : bond 0.04276 ( 548) hydrogen bonds : angle 5.89216 ( 1509) link_BETA1-4 : bond 0.00557 ( 34) link_BETA1-4 : angle 2.26140 ( 102) link_NAG-ASN : bond 0.00342 ( 51) link_NAG-ASN : angle 2.85388 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8030 (p0) cc_final: 0.7765 (p0) REVERT: A 265 LEU cc_start: 0.8639 (mp) cc_final: 0.8168 (tp) REVERT: D 601 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8701 (ttmm) REVERT: D 633 LYS cc_start: 0.8642 (mttt) cc_final: 0.8420 (mptt) REVERT: D 652 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8633 (tp-100) REVERT: D 656 ASN cc_start: 0.8607 (m-40) cc_final: 0.8108 (m-40) REVERT: E 153 MET cc_start: 0.8136 (tpp) cc_final: 0.7564 (tpp) REVERT: E 364 SER cc_start: 0.8964 (t) cc_final: 0.8630 (p) REVERT: E 426 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7399 (ptt) REVERT: F 530 MET cc_start: 0.7552 (mmt) cc_final: 0.7266 (tpp) REVERT: F 621 GLU cc_start: 0.8225 (pt0) cc_final: 0.7853 (tp30) REVERT: F 634 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8166 (tt0) REVERT: G 92 ASP cc_start: 0.8538 (t0) cc_final: 0.8257 (t0) REVERT: H 79 SER cc_start: 0.9250 (p) cc_final: 0.8734 (m) REVERT: I 53 LYS cc_start: 0.8884 (mttt) cc_final: 0.8663 (mttm) REVERT: I 110 LYS cc_start: 0.8427 (tmtt) cc_final: 0.7869 (tptp) REVERT: I 138 ASP cc_start: 0.7082 (m-30) cc_final: 0.6270 (p0) REVERT: I 180 LEU cc_start: 0.5139 (tp) cc_final: 0.4885 (tt) REVERT: J 166 PHE cc_start: 0.7736 (m-80) cc_final: 0.7256 (m-80) outliers start: 28 outliers final: 15 residues processed: 298 average time/residue: 0.1471 time to fit residues: 68.2739 Evaluate side-chains 262 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 246 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain I residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.084754 restraints weight = 43955.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087599 restraints weight = 23191.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089479 restraints weight = 15943.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.090622 restraints weight = 12654.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091232 restraints weight = 11050.533| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 20191 Z= 0.347 Angle : 0.888 13.421 27608 Z= 0.423 Chirality : 0.052 0.329 3354 Planarity : 0.005 0.065 3341 Dihedral : 9.350 108.000 4341 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.74 % Favored : 92.17 % Rotamer: Outliers : 2.26 % Allowed : 11.29 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.17), residues: 2300 helix: 0.50 (0.30), residues: 318 sheet: -0.68 (0.20), residues: 688 loop : -1.82 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 170 TYR 0.025 0.002 TYR E 484 PHE 0.038 0.003 PHE E 53 TRP 0.034 0.002 TRP E 112 HIS 0.009 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00817 (20070) covalent geometry : angle 0.83092 (27281) SS BOND : bond 0.01393 ( 36) SS BOND : angle 3.09842 ( 72) hydrogen bonds : bond 0.05256 ( 548) hydrogen bonds : angle 5.79706 ( 1509) link_BETA1-4 : bond 0.00544 ( 34) link_BETA1-4 : angle 2.44386 ( 102) link_NAG-ASN : bond 0.00561 ( 51) link_NAG-ASN : angle 3.26687 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 241 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.8813 (mp) cc_final: 0.8303 (tp) REVERT: B 584 GLU cc_start: 0.9008 (tp30) cc_final: 0.8494 (tp30) REVERT: B 640 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7834 (tp40) REVERT: C 95 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8220 (ttp) REVERT: C 116 LEU cc_start: 0.8952 (tp) cc_final: 0.8749 (tp) REVERT: C 158 ARG cc_start: 0.8306 (ttp80) cc_final: 0.7691 (tmm-80) REVERT: D 633 LYS cc_start: 0.8843 (mttt) cc_final: 0.8620 (mptt) REVERT: D 652 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8654 (tp-100) REVERT: D 655 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8737 (mmmt) REVERT: D 656 ASN cc_start: 0.8504 (m-40) cc_final: 0.8157 (m-40) REVERT: E 153 MET cc_start: 0.8334 (tpp) cc_final: 0.7782 (tpp) REVERT: E 353 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.7336 (t80) REVERT: F 530 MET cc_start: 0.7745 (mmt) cc_final: 0.7431 (tpp) REVERT: F 621 GLU cc_start: 0.8371 (pt0) cc_final: 0.7969 (tp30) REVERT: F 624 ASP cc_start: 0.7836 (m-30) cc_final: 0.7575 (m-30) REVERT: F 634 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8763 (tt0) REVERT: G 39 LYS cc_start: 0.8362 (mttt) cc_final: 0.7938 (mmtt) REVERT: G 87 TYR cc_start: 0.8961 (m-80) cc_final: 0.8714 (m-80) REVERT: G 92 ASP cc_start: 0.8997 (t0) cc_final: 0.8696 (t70) REVERT: H 102 ASN cc_start: 0.8553 (m-40) cc_final: 0.8225 (t0) outliers start: 47 outliers final: 33 residues processed: 274 average time/residue: 0.1457 time to fit residues: 61.3044 Evaluate side-chains 250 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain I residue 2 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 139 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 144 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 130 GLN E 67 ASN F 653 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 ASN I 169 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.119487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.089062 restraints weight = 43243.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.092052 restraints weight = 22267.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094038 restraints weight = 15104.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095246 restraints weight = 11893.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095957 restraints weight = 10306.739| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20191 Z= 0.125 Angle : 0.701 12.812 27608 Z= 0.329 Chirality : 0.046 0.328 3354 Planarity : 0.004 0.052 3341 Dihedral : 8.644 106.360 4341 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 2.02 % Allowed : 13.65 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.17), residues: 2300 helix: 1.10 (0.31), residues: 319 sheet: -0.48 (0.21), residues: 686 loop : -1.69 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 81 TYR 0.013 0.001 TYR H 50 PHE 0.030 0.001 PHE F 522 TRP 0.017 0.001 TRP C 112 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00280 (20070) covalent geometry : angle 0.64984 (27281) SS BOND : bond 0.00735 ( 36) SS BOND : angle 2.45945 ( 72) hydrogen bonds : bond 0.03747 ( 548) hydrogen bonds : angle 5.17439 ( 1509) link_BETA1-4 : bond 0.00535 ( 34) link_BETA1-4 : angle 2.14049 ( 102) link_NAG-ASN : bond 0.00302 ( 51) link_NAG-ASN : angle 2.75208 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8943 (tpp) cc_final: 0.8513 (tpp) REVERT: A 265 LEU cc_start: 0.8796 (mp) cc_final: 0.8237 (tp) REVERT: B 640 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7552 (tp40) REVERT: C 158 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7519 (tmm-80) REVERT: D 633 LYS cc_start: 0.8694 (mttt) cc_final: 0.8475 (mptt) REVERT: D 652 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8494 (tp-100) REVERT: D 655 LYS cc_start: 0.8943 (mtpp) cc_final: 0.8739 (mmmt) REVERT: D 656 ASN cc_start: 0.8541 (m-40) cc_final: 0.7950 (m-40) REVERT: E 153 MET cc_start: 0.8052 (tpp) cc_final: 0.7454 (tpp) REVERT: E 364 SER cc_start: 0.9176 (t) cc_final: 0.8874 (p) REVERT: F 530 MET cc_start: 0.7541 (mmt) cc_final: 0.7182 (tpp) REVERT: F 621 GLU cc_start: 0.8330 (pt0) cc_final: 0.7894 (tp30) REVERT: G 92 ASP cc_start: 0.8791 (t0) cc_final: 0.8415 (t0) REVERT: H 102 ASN cc_start: 0.8511 (m-40) cc_final: 0.8259 (t0) outliers start: 42 outliers final: 25 residues processed: 283 average time/residue: 0.1461 time to fit residues: 63.4065 Evaluate side-chains 266 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain I residue 2 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 27 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 139 optimal weight: 0.0370 chunk 57 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 overall best weight: 2.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN F 653 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 ASN I 112 ASN ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.116874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.086376 restraints weight = 43607.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089271 restraints weight = 22797.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.091168 restraints weight = 15616.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.092339 restraints weight = 12383.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093048 restraints weight = 10775.860| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20191 Z= 0.221 Angle : 0.759 13.131 27608 Z= 0.355 Chirality : 0.048 0.314 3354 Planarity : 0.004 0.049 3341 Dihedral : 8.715 104.769 4341 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.43 % Favored : 92.48 % Rotamer: Outliers : 2.26 % Allowed : 15.09 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.18), residues: 2300 helix: 0.77 (0.30), residues: 327 sheet: -0.48 (0.21), residues: 679 loop : -1.71 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 469 TYR 0.018 0.001 TYR E 484 PHE 0.026 0.002 PHE E 53 TRP 0.021 0.001 TRP E 112 HIS 0.007 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00522 (20070) covalent geometry : angle 0.70490 (27281) SS BOND : bond 0.00929 ( 36) SS BOND : angle 2.86870 ( 72) hydrogen bonds : bond 0.04066 ( 548) hydrogen bonds : angle 5.16432 ( 1509) link_BETA1-4 : bond 0.00503 ( 34) link_BETA1-4 : angle 2.19925 ( 102) link_NAG-ASN : bond 0.00409 ( 51) link_NAG-ASN : angle 2.88306 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.8804 (mp) cc_final: 0.8264 (tp) REVERT: A 475 MET cc_start: 0.8234 (mmm) cc_final: 0.8004 (mmm) REVERT: B 640 GLN cc_start: 0.8030 (tp-100) cc_final: 0.7663 (tp40) REVERT: C 153 MET cc_start: 0.7593 (mmm) cc_final: 0.7359 (tpt) REVERT: C 158 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7491 (tmm-80) REVERT: D 579 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7401 (ptt180) REVERT: D 630 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8934 (pm20) REVERT: D 633 LYS cc_start: 0.8774 (mttt) cc_final: 0.8567 (mptt) REVERT: D 652 GLN cc_start: 0.8917 (tp-100) cc_final: 0.8425 (tp-100) REVERT: D 655 LYS cc_start: 0.8942 (mtpp) cc_final: 0.8733 (mmmt) REVERT: D 656 ASN cc_start: 0.8419 (m-40) cc_final: 0.7764 (m-40) REVERT: E 153 MET cc_start: 0.8206 (tpp) cc_final: 0.7501 (tpp) REVERT: F 530 MET cc_start: 0.7652 (mmt) cc_final: 0.7359 (tpp) REVERT: F 621 GLU cc_start: 0.8379 (pt0) cc_final: 0.7903 (tp30) REVERT: G 39 LYS cc_start: 0.8341 (mttt) cc_final: 0.7943 (mmtt) REVERT: G 92 ASP cc_start: 0.8979 (t0) cc_final: 0.8495 (t70) REVERT: G 162 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7116 (p) REVERT: J 171 GLN cc_start: 0.7974 (mp10) cc_final: 0.7514 (mp10) outliers start: 47 outliers final: 32 residues processed: 272 average time/residue: 0.1478 time to fit residues: 61.1421 Evaluate side-chains 263 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain I residue 2 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 99 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 204 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 178 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 ASN I 112 ASN I 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.119265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088902 restraints weight = 42990.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.091892 restraints weight = 22138.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093803 restraints weight = 15012.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095014 restraints weight = 11899.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.095695 restraints weight = 10301.010| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20191 Z= 0.123 Angle : 0.695 12.961 27608 Z= 0.324 Chirality : 0.046 0.316 3354 Planarity : 0.004 0.046 3341 Dihedral : 8.327 102.519 4341 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.26 % Rotamer: Outliers : 1.97 % Allowed : 16.05 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.18), residues: 2300 helix: 1.22 (0.31), residues: 321 sheet: -0.37 (0.21), residues: 672 loop : -1.57 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 469 TYR 0.019 0.001 TYR A 484 PHE 0.022 0.001 PHE F 522 TRP 0.019 0.001 TRP F 610 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00281 (20070) covalent geometry : angle 0.64567 (27281) SS BOND : bond 0.00656 ( 36) SS BOND : angle 2.51352 ( 72) hydrogen bonds : bond 0.03418 ( 548) hydrogen bonds : angle 4.87607 ( 1509) link_BETA1-4 : bond 0.00549 ( 34) link_BETA1-4 : angle 2.05517 ( 102) link_NAG-ASN : bond 0.00308 ( 51) link_NAG-ASN : angle 2.66516 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.8782 (mp) cc_final: 0.8217 (tp) REVERT: A 475 MET cc_start: 0.8238 (mmm) cc_final: 0.7959 (mmm) REVERT: B 657 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 158 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7413 (tmm-80) REVERT: C 457 ASP cc_start: 0.8427 (t0) cc_final: 0.8195 (t0) REVERT: D 579 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7289 (ptt180) REVERT: D 633 LYS cc_start: 0.8706 (mttt) cc_final: 0.8407 (mptt) REVERT: D 652 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8381 (tp-100) REVERT: D 655 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8701 (mmmt) REVERT: D 656 ASN cc_start: 0.8533 (m-40) cc_final: 0.7875 (m-40) REVERT: E 153 MET cc_start: 0.8208 (tpp) cc_final: 0.7582 (tpp) REVERT: E 364 SER cc_start: 0.9154 (t) cc_final: 0.8853 (p) REVERT: F 530 MET cc_start: 0.7473 (mmt) cc_final: 0.7237 (tpp) REVERT: F 621 GLU cc_start: 0.8442 (pt0) cc_final: 0.7958 (tp30) REVERT: F 655 LYS cc_start: 0.9225 (pttt) cc_final: 0.9025 (pttp) REVERT: G 39 LYS cc_start: 0.8294 (mttt) cc_final: 0.7905 (mmtt) REVERT: G 92 ASP cc_start: 0.8835 (t0) cc_final: 0.8412 (t0) REVERT: H 29 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7597 (mpp) REVERT: I 110 LYS cc_start: 0.8475 (tttm) cc_final: 0.8026 (tptp) REVERT: J 171 GLN cc_start: 0.7997 (mp10) cc_final: 0.7562 (mp10) outliers start: 41 outliers final: 29 residues processed: 279 average time/residue: 0.1531 time to fit residues: 65.1981 Evaluate side-chains 268 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 2 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 188 HIS Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 8 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086990 restraints weight = 43489.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089891 restraints weight = 22721.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091792 restraints weight = 15594.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.092970 restraints weight = 12392.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093659 restraints weight = 10768.375| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20191 Z= 0.190 Angle : 0.739 13.123 27608 Z= 0.345 Chirality : 0.047 0.307 3354 Planarity : 0.004 0.047 3341 Dihedral : 8.359 99.822 4341 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.39 % Favored : 92.52 % Rotamer: Outliers : 2.35 % Allowed : 16.87 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.18), residues: 2300 helix: 1.06 (0.31), residues: 327 sheet: -0.39 (0.21), residues: 679 loop : -1.56 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 469 TYR 0.016 0.001 TYR E 484 PHE 0.024 0.002 PHE E 53 TRP 0.018 0.001 TRP E 112 HIS 0.004 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00447 (20070) covalent geometry : angle 0.68328 (27281) SS BOND : bond 0.00978 ( 36) SS BOND : angle 3.06470 ( 72) hydrogen bonds : bond 0.03750 ( 548) hydrogen bonds : angle 4.91949 ( 1509) link_BETA1-4 : bond 0.00505 ( 34) link_BETA1-4 : angle 2.11744 ( 102) link_NAG-ASN : bond 0.00386 ( 51) link_NAG-ASN : angle 2.78970 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.8805 (mp) cc_final: 0.8244 (tp) REVERT: A 475 MET cc_start: 0.8293 (mmm) cc_final: 0.8003 (mmm) REVERT: B 657 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 158 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7540 (tmm-80) REVERT: C 373 THR cc_start: 0.8605 (p) cc_final: 0.8393 (p) REVERT: C 457 ASP cc_start: 0.8508 (t0) cc_final: 0.8252 (t0) REVERT: D 579 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7358 (ptt180) REVERT: D 633 LYS cc_start: 0.8767 (mttt) cc_final: 0.8525 (mptt) REVERT: D 652 GLN cc_start: 0.8891 (tp-100) cc_final: 0.8369 (tp-100) REVERT: D 656 ASN cc_start: 0.8578 (m-40) cc_final: 0.7777 (m-40) REVERT: E 153 MET cc_start: 0.8248 (tpp) cc_final: 0.7556 (tpp) REVERT: E 364 SER cc_start: 0.9227 (t) cc_final: 0.8894 (p) REVERT: F 621 GLU cc_start: 0.8502 (pt0) cc_final: 0.8023 (tp30) REVERT: F 654 GLU cc_start: 0.8360 (pp20) cc_final: 0.8159 (pp20) REVERT: G 39 LYS cc_start: 0.8286 (mttt) cc_final: 0.7889 (mmtt) REVERT: G 92 ASP cc_start: 0.8999 (t0) cc_final: 0.8667 (t70) REVERT: G 171 LYS cc_start: 0.6839 (mmmt) cc_final: 0.6623 (tppt) REVERT: H 29 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7638 (mpp) REVERT: J 171 GLN cc_start: 0.7906 (mp10) cc_final: 0.7445 (mp10) outliers start: 49 outliers final: 37 residues processed: 275 average time/residue: 0.1504 time to fit residues: 62.6478 Evaluate side-chains 272 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 2 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 188 HIS Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 113 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN I 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.117783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087445 restraints weight = 43429.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090376 restraints weight = 22601.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092249 restraints weight = 15408.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093356 restraints weight = 12260.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094150 restraints weight = 10708.603| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20191 Z= 0.164 Angle : 0.728 13.250 27608 Z= 0.340 Chirality : 0.047 0.306 3354 Planarity : 0.004 0.046 3341 Dihedral : 8.276 97.216 4341 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.48 % Favored : 93.43 % Rotamer: Outliers : 2.40 % Allowed : 17.44 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.18), residues: 2300 helix: 1.08 (0.31), residues: 328 sheet: -0.40 (0.21), residues: 681 loop : -1.54 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 105 TYR 0.018 0.001 TYR A 484 PHE 0.023 0.002 PHE E 53 TRP 0.019 0.001 TRP F 610 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00385 (20070) covalent geometry : angle 0.67245 (27281) SS BOND : bond 0.00810 ( 36) SS BOND : angle 3.16041 ( 72) hydrogen bonds : bond 0.03611 ( 548) hydrogen bonds : angle 4.82139 ( 1509) link_BETA1-4 : bond 0.00514 ( 34) link_BETA1-4 : angle 2.07865 ( 102) link_NAG-ASN : bond 0.00335 ( 51) link_NAG-ASN : angle 2.73479 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.8784 (mp) cc_final: 0.8232 (tp) REVERT: A 475 MET cc_start: 0.8266 (mmm) cc_final: 0.7980 (mmm) REVERT: B 657 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8415 (tm-30) REVERT: C 158 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7541 (tmm-80) REVERT: C 457 ASP cc_start: 0.8460 (t0) cc_final: 0.8211 (t0) REVERT: D 579 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7340 (ptt180) REVERT: D 633 LYS cc_start: 0.8723 (mttt) cc_final: 0.8506 (mptt) REVERT: D 652 GLN cc_start: 0.8934 (tp-100) cc_final: 0.8411 (tp-100) REVERT: D 656 ASN cc_start: 0.8586 (m-40) cc_final: 0.7800 (m-40) REVERT: E 153 MET cc_start: 0.8265 (tpp) cc_final: 0.7606 (tpp) REVERT: E 364 SER cc_start: 0.9214 (t) cc_final: 0.8866 (p) REVERT: F 621 GLU cc_start: 0.8507 (pt0) cc_final: 0.8004 (tp30) REVERT: G 39 LYS cc_start: 0.8278 (mttt) cc_final: 0.7885 (mmtt) REVERT: G 92 ASP cc_start: 0.8994 (t0) cc_final: 0.8664 (t70) REVERT: H 29 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7611 (mpp) REVERT: J 171 GLN cc_start: 0.7977 (mp10) cc_final: 0.7559 (mp10) outliers start: 50 outliers final: 40 residues processed: 264 average time/residue: 0.1503 time to fit residues: 60.1982 Evaluate side-chains 276 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 2 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 188 HIS Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 chunk 163 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.088745 restraints weight = 43018.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091724 restraints weight = 22201.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.093634 restraints weight = 15063.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.094851 restraints weight = 11947.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095477 restraints weight = 10319.270| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20191 Z= 0.129 Angle : 0.705 13.026 27608 Z= 0.327 Chirality : 0.046 0.308 3354 Planarity : 0.004 0.044 3341 Dihedral : 7.960 93.006 4341 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.65 % Favored : 93.30 % Rotamer: Outliers : 2.11 % Allowed : 17.49 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.18), residues: 2300 helix: 1.02 (0.31), residues: 336 sheet: -0.29 (0.21), residues: 670 loop : -1.41 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 105 TYR 0.011 0.001 TYR E 484 PHE 0.019 0.001 PHE E 53 TRP 0.035 0.001 TRP F 623 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00297 (20070) covalent geometry : angle 0.65406 (27281) SS BOND : bond 0.00636 ( 36) SS BOND : angle 2.86888 ( 72) hydrogen bonds : bond 0.03309 ( 548) hydrogen bonds : angle 4.67552 ( 1509) link_BETA1-4 : bond 0.00523 ( 34) link_BETA1-4 : angle 2.02611 ( 102) link_NAG-ASN : bond 0.00339 ( 51) link_NAG-ASN : angle 2.62762 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.8768 (mp) cc_final: 0.8219 (tp) REVERT: A 475 MET cc_start: 0.8259 (mmm) cc_final: 0.8036 (mmm) REVERT: B 657 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8437 (tm-30) REVERT: C 153 MET cc_start: 0.8009 (mmm) cc_final: 0.7790 (tpt) REVERT: C 158 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7503 (tmm-80) REVERT: C 457 ASP cc_start: 0.8363 (t0) cc_final: 0.8132 (t0) REVERT: D 579 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7167 (ptt180) REVERT: D 652 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8480 (tp-100) REVERT: D 656 ASN cc_start: 0.8611 (m-40) cc_final: 0.7942 (m-40) REVERT: E 153 MET cc_start: 0.8235 (tpp) cc_final: 0.7609 (tpp) REVERT: E 364 SER cc_start: 0.9179 (t) cc_final: 0.8825 (p) REVERT: F 621 GLU cc_start: 0.8540 (pt0) cc_final: 0.8032 (tp30) REVERT: F 654 GLU cc_start: 0.8478 (pp20) cc_final: 0.8194 (pp20) REVERT: G 39 LYS cc_start: 0.8288 (mttt) cc_final: 0.7867 (mmtt) REVERT: G 92 ASP cc_start: 0.8954 (t0) cc_final: 0.8485 (t70) REVERT: H 79 SER cc_start: 0.9313 (p) cc_final: 0.8777 (m) REVERT: I 156 LYS cc_start: 0.7125 (mmtt) cc_final: 0.6681 (tppt) REVERT: J 59 TYR cc_start: 0.9376 (m-80) cc_final: 0.9153 (m-80) REVERT: J 171 GLN cc_start: 0.7978 (mp10) cc_final: 0.7566 (mp10) outliers start: 44 outliers final: 36 residues processed: 284 average time/residue: 0.1518 time to fit residues: 66.1549 Evaluate side-chains 277 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 2 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 HIS Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 183 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 147 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN I 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.119817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.089658 restraints weight = 42990.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092644 restraints weight = 22130.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094610 restraints weight = 15013.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095820 restraints weight = 11822.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096411 restraints weight = 10235.419| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20191 Z= 0.120 Angle : 0.697 12.914 27608 Z= 0.325 Chirality : 0.046 0.311 3354 Planarity : 0.004 0.043 3341 Dihedral : 7.734 87.848 4341 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.26 % Favored : 93.70 % Rotamer: Outliers : 1.83 % Allowed : 18.26 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.18), residues: 2300 helix: 1.11 (0.31), residues: 336 sheet: -0.26 (0.21), residues: 670 loop : -1.36 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 81 TYR 0.019 0.001 TYR A 484 PHE 0.023 0.001 PHE B 522 TRP 0.047 0.001 TRP F 623 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00275 (20070) covalent geometry : angle 0.65132 (27281) SS BOND : bond 0.00586 ( 36) SS BOND : angle 2.46466 ( 72) hydrogen bonds : bond 0.03155 ( 548) hydrogen bonds : angle 4.59021 ( 1509) link_BETA1-4 : bond 0.00542 ( 34) link_BETA1-4 : angle 2.01601 ( 102) link_NAG-ASN : bond 0.00297 ( 51) link_NAG-ASN : angle 2.54773 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.8760 (mp) cc_final: 0.8200 (tp) REVERT: A 475 MET cc_start: 0.8269 (mmm) cc_final: 0.8029 (mmm) REVERT: B 589 ASP cc_start: 0.8801 (t0) cc_final: 0.8278 (t0) REVERT: B 657 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8515 (tm-30) REVERT: C 153 MET cc_start: 0.7896 (mmm) cc_final: 0.7607 (tpt) REVERT: C 158 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7468 (tmm-80) REVERT: D 579 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7135 (ptt180) REVERT: D 633 LYS cc_start: 0.8471 (mptt) cc_final: 0.8245 (mmtm) REVERT: D 652 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8661 (tp-100) REVERT: D 656 ASN cc_start: 0.8455 (m-40) cc_final: 0.8149 (m-40) REVERT: E 143 ARG cc_start: 0.7955 (tpt170) cc_final: 0.7650 (tpt170) REVERT: E 153 MET cc_start: 0.8223 (tpp) cc_final: 0.7598 (tpp) REVERT: E 364 SER cc_start: 0.9221 (t) cc_final: 0.8839 (p) REVERT: F 621 GLU cc_start: 0.8498 (pt0) cc_final: 0.8019 (tp30) REVERT: F 654 GLU cc_start: 0.8494 (pp20) cc_final: 0.8230 (pp20) REVERT: G 92 ASP cc_start: 0.8914 (t0) cc_final: 0.8499 (t0) REVERT: H 29 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7531 (mpp) REVERT: H 79 SER cc_start: 0.9300 (p) cc_final: 0.8760 (m) REVERT: I 110 LYS cc_start: 0.8323 (tttm) cc_final: 0.7860 (tmtt) REVERT: I 156 LYS cc_start: 0.7091 (mmtt) cc_final: 0.6620 (tppt) REVERT: I 178 LEU cc_start: 0.9114 (tt) cc_final: 0.8694 (tp) REVERT: J 59 TYR cc_start: 0.9358 (m-80) cc_final: 0.9137 (m-80) REVERT: J 171 GLN cc_start: 0.7927 (mp10) cc_final: 0.7501 (mp10) outliers start: 38 outliers final: 35 residues processed: 280 average time/residue: 0.1489 time to fit residues: 64.0119 Evaluate side-chains 281 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 2 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 119 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 216 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.115960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085414 restraints weight = 43730.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088285 restraints weight = 23059.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090177 restraints weight = 15867.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091368 restraints weight = 12607.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.092029 restraints weight = 10966.891| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20191 Z= 0.234 Angle : 0.787 13.232 27608 Z= 0.369 Chirality : 0.048 0.332 3354 Planarity : 0.004 0.047 3341 Dihedral : 8.047 83.829 4341 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.61 % Favored : 92.30 % Rotamer: Outliers : 2.26 % Allowed : 18.31 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.18), residues: 2300 helix: 0.78 (0.30), residues: 338 sheet: -0.46 (0.20), residues: 694 loop : -1.46 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 81 TYR 0.017 0.001 TYR E 484 PHE 0.029 0.002 PHE E 53 TRP 0.053 0.002 TRP D 571 HIS 0.005 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00552 (20070) covalent geometry : angle 0.73740 (27281) SS BOND : bond 0.00924 ( 36) SS BOND : angle 2.67314 ( 72) hydrogen bonds : bond 0.03952 ( 548) hydrogen bonds : angle 4.86221 ( 1509) link_BETA1-4 : bond 0.00479 ( 34) link_BETA1-4 : angle 2.19126 ( 102) link_NAG-ASN : bond 0.00411 ( 51) link_NAG-ASN : angle 2.85881 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3424.35 seconds wall clock time: 60 minutes 8.46 seconds (3608.46 seconds total)