Starting phenix.real_space_refine on Thu Sep 18 18:30:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mla_48351/09_2025/9mla_48351.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mla_48351/09_2025/9mla_48351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mla_48351/09_2025/9mla_48351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mla_48351/09_2025/9mla_48351.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mla_48351/09_2025/9mla_48351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mla_48351/09_2025/9mla_48351.map" } resolution = 2.24 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= 0.015 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 102 5.16 5 C 11820 2.51 5 N 3051 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 18633 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2882 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2882 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2882 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "E" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "F" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "G" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 950 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 950 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 950 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "J" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "K" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" 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: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "i" 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: "j" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" 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: "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: 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: "D" 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: "E" 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: "F" 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 Time building chain proxies: 3.86, per 1000 atoms: 0.21 Number of scatterers: 18633 At special positions: 0 Unit cell: (115.029, 114.086, 162.172, 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 102 16.00 O 3660 8.00 N 3051 7.00 C 11820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 171 " distance=2.04 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 282 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 413 " distance=2.03 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 408 " distance=2.02 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS D 498 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 171 " distance=2.04 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 282 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 413 " distance=2.03 Simple disulfide: pdb=" SG CYS B 405 " - pdb=" SG CYS B 408 " distance=2.02 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS E 498 " distance=2.04 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 171 " distance=2.04 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 282 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 413 " distance=2.03 Simple disulfide: pdb=" SG CYS C 405 " - pdb=" SG CYS C 408 " distance=2.02 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS F 498 " distance=2.03 Simple disulfide: pdb=" SG CYS D 551 " - pdb=" SG CYS D 559 " distance=2.03 Simple disulfide: pdb=" SG CYS E 551 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS F 551 " - pdb=" SG CYS F 559 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA R 3 " - " MAN R 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " 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 b 2 " - " BMA b 3 " " 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 e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " 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 i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " BETA1-6 " NAG d 1 " - " FUC d 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG g 1 " - " FUC g 4 " " NAG j 1 " - " FUC j 4 " NAG-ASN " NAG A 501 " - " ASN A 100 " " NAG B 501 " - " ASN B 100 " " NAG C 501 " - " ASN C 100 " " NAG D 801 " - " ASN D 585 " " NAG E 801 " - " ASN E 585 " " NAG F 801 " - " ASN F 585 " " NAG M 1 " - " ASN A 128 " " NAG N 1 " - " ASN A 274 " " NAG O 1 " - " ASN A 355 " " NAG P 1 " - " ASN A 372 " " NAG Q 1 " - " ASN A 153 " " NAG R 1 " - " ASN B 128 " " NAG S 1 " - " ASN B 274 " " NAG T 1 " - " ASN B 355 " " NAG U 1 " - " ASN B 372 " " NAG V 1 " - " ASN B 153 " " NAG W 1 " - " ASN C 128 " " NAG X 1 " - " ASN C 274 " " NAG Y 1 " - " ASN C 355 " " NAG Z 1 " - " ASN C 372 " " NAG a 1 " - " ASN C 153 " " NAG b 1 " - " ASN D 507 " " NAG c 1 " - " ASN D 554 " " NAG d 1 " - " ASN D 566 " " NAG e 1 " - " ASN E 507 " " NAG f 1 " - " ASN E 554 " " NAG g 1 " - " ASN E 566 " " NAG h 1 " - " ASN F 507 " " NAG i 1 " - " ASN F 554 " " NAG j 1 " - " ASN F 566 " Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 749.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4164 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 42 sheets defined 18.0% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.717A pdb=" N GLU A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.699A pdb=" N THR A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.864A pdb=" N LEU A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 459 Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.674A pdb=" N GLU B 148 " --> pdb=" O PRO B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.555A pdb=" N THR B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.861A pdb=" N LEU B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 345 " --> pdb=" O ARG B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 459 removed outlier: 3.697A pdb=" N GLU B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.672A pdb=" N THR C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.933A pdb=" N LEU C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 345 " --> pdb=" O ARG C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'D' and resid 476 through 492 removed outlier: 4.432A pdb=" N VAL D 486 " --> pdb=" O ALA D 482 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA D 490 " --> pdb=" O VAL D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 512 removed outlier: 5.172A pdb=" N ASN D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N SER D 508 " --> pdb=" O TRP D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 524 Processing helix chain 'D' and resid 529 through 548 removed outlier: 3.845A pdb=" N GLN D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 580 Processing helix chain 'D' and resid 589 through 599 Processing helix chain 'D' and resid 602 through 607 Processing helix chain 'D' and resid 610 through 618 removed outlier: 3.550A pdb=" N ALA D 618 " --> pdb=" O ILE D 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 492 removed outlier: 4.450A pdb=" N VAL E 486 " --> pdb=" O ALA E 482 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA E 487 " --> pdb=" O THR E 483 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA E 490 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 512 removed outlier: 5.093A pdb=" N ASN E 507 " --> pdb=" O ASP E 503 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N SER E 508 " --> pdb=" O TRP E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 524 Processing helix chain 'E' and resid 529 through 549 removed outlier: 3.713A pdb=" N GLN E 548 " --> pdb=" O GLU E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 580 Processing helix chain 'E' and resid 589 through 599 Processing helix chain 'E' and resid 602 through 607 Processing helix chain 'E' and resid 610 through 618 Processing helix chain 'F' and resid 476 through 492 removed outlier: 4.516A pdb=" N VAL F 486 " --> pdb=" O ALA F 482 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA F 487 " --> pdb=" O THR F 483 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA F 490 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 512 removed outlier: 5.140A pdb=" N ASN F 507 " --> pdb=" O ASP F 503 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER F 508 " --> pdb=" O TRP F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 524 Processing helix chain 'F' and resid 529 through 548 removed outlier: 3.735A pdb=" N GLN F 548 " --> pdb=" O GLU F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 581 removed outlier: 3.506A pdb=" N VAL F 575 " --> pdb=" O HIS F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 599 Processing helix chain 'F' and resid 602 through 607 Processing helix chain 'F' and resid 610 through 618 Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.138A pdb=" N THR G 91 " --> pdb=" O ASN G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.707A pdb=" N ASP I 90 " --> pdb=" O LYS I 87 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR I 91 " --> pdb=" O ASN I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'J' and resid 82 through 86 removed outlier: 3.702A pdb=" N ASP J 85 " --> pdb=" O GLU J 82 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL J 86 " --> pdb=" O ALA J 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 82 through 86' Processing helix chain 'K' and resid 82 through 86 removed outlier: 3.754A pdb=" N VAL K 86 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 Processing sheet with id=AA1, first strand: chain 'D' and resid 496 through 497 removed outlier: 4.538A pdb=" N GLN D 496 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 102 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN D 563 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP A 104 " --> pdb=" O THR D 561 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 157 removed outlier: 6.082A pdb=" N MET A 150 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG A 409 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE A 152 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 407 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 184 removed outlier: 5.937A pdb=" N SER A 190 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 358 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 192 " --> pdb=" O GLN A 356 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 349 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR A 376 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE A 351 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER A 374 " --> pdb=" O ILE A 351 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 206 through 207 removed outlier: 3.652A pdb=" N SER A 213 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 216 through 217 removed outlier: 6.261A pdb=" N ILE A 262 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN A 256 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY A 260 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 329 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 263 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE A 327 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 270 through 272 Processing sheet with id=AA9, first strand: chain 'E' and resid 496 through 497 removed outlier: 4.538A pdb=" N GLN E 496 " --> pdb=" O PRO B 436 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 102 " --> pdb=" O GLN E 563 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN E 563 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP B 104 " --> pdb=" O THR E 561 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AB2, first strand: chain 'B' and resid 150 through 157 removed outlier: 6.104A pdb=" N MET B 150 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG B 409 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE B 152 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN B 407 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AB4, first strand: chain 'B' and resid 174 through 184 removed outlier: 5.895A pdb=" N SER B 190 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 358 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 192 " --> pdb=" O GLN B 356 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE B 349 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR B 376 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE B 351 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER B 374 " --> pdb=" O ILE B 351 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 206 through 207 removed outlier: 3.669A pdb=" N SER B 213 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 216 through 217 removed outlier: 6.237A pdb=" N ILE B 262 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN B 256 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY B 260 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR B 261 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 270 through 272 Processing sheet with id=AB8, first strand: chain 'F' and resid 496 through 497 removed outlier: 4.774A pdb=" N GLN F 496 " --> pdb=" O PRO C 436 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR C 102 " --> pdb=" O GLN F 563 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN F 563 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TRP C 104 " --> pdb=" O THR F 561 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AC1, first strand: chain 'C' and resid 150 through 157 removed outlier: 6.082A pdb=" N MET C 150 " --> pdb=" O ARG C 409 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG C 409 " --> pdb=" O MET C 150 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE C 152 " --> pdb=" O ASN C 407 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN C 407 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AC3, first strand: chain 'C' and resid 174 through 184 removed outlier: 5.904A pdb=" N SER C 190 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU C 358 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 192 " --> pdb=" O GLN C 356 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 349 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C 376 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE C 351 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER C 374 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 206 through 207 removed outlier: 3.716A pdb=" N SER C 213 " --> pdb=" O ASN C 207 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 216 through 217 removed outlier: 6.206A pdb=" N ILE C 262 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN C 256 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY C 260 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 329 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE C 263 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE C 327 " --> pdb=" O ILE C 263 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.538A pdb=" N VAL G 83 " --> pdb=" O VAL G 18 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 11 removed outlier: 7.179A pdb=" N GLU G 10 " --> pdb=" O THR G 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.923A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL G 110 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.634A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.869A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.953A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL H 110 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.365A pdb=" N GLU I 10 " --> pdb=" O THR I 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AD6, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.939A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL I 110 " --> pdb=" O LYS I 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'J' and resid 29 through 30 Processing sheet with id=AD9, first strand: chain 'J' and resid 56 through 57 removed outlier: 6.529A pdb=" N TRP J 38 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR J 52 " --> pdb=" O MET J 36 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET J 36 " --> pdb=" O TYR J 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'K' and resid 29 through 30 Processing sheet with id=AE3, first strand: chain 'K' and resid 56 through 57 removed outlier: 6.540A pdb=" N TRP K 38 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR K 52 " --> pdb=" O MET K 36 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET K 36 " --> pdb=" O TYR K 52 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'L' and resid 29 through 30 Processing sheet with id=AE6, first strand: chain 'L' and resid 56 through 57 removed outlier: 6.524A pdb=" N TRP L 38 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR L 52 " --> pdb=" O MET L 36 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET L 36 " --> pdb=" O TYR L 52 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1710 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: 3.23 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5709 1.34 - 1.46: 4123 1.46 - 1.58: 9152 1.58 - 1.70: 0 1.70 - 1.81: 147 Bond restraints: 19131 Sorted by residual: bond pdb=" CB CYS B 246 " pdb=" SG CYS B 246 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB CYS A 246 " pdb=" SG CYS A 246 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB CYS C 246 " pdb=" SG CYS C 246 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" C ASN K 79 " pdb=" N PRO K 80 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.78e-01 bond pdb=" CB CYS C 437 " pdb=" SG CYS C 437 " ideal model delta sigma weight residual 1.808 1.779 0.029 3.30e-02 9.18e+02 7.49e-01 ... (remaining 19126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 25754 1.99 - 3.99: 299 3.99 - 5.98: 23 5.98 - 7.98: 0 7.98 - 9.97: 6 Bond angle restraints: 26082 Sorted by residual: angle pdb=" C2 NAG V 1 " pdb=" N2 NAG V 1 " pdb=" C7 NAG V 1 " ideal model delta sigma weight residual 124.56 134.53 -9.97 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C2 NAG Q 1 " pdb=" N2 NAG Q 1 " pdb=" C7 NAG Q 1 " ideal model delta sigma weight residual 124.56 134.50 -9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C2 NAG a 1 " pdb=" N2 NAG a 1 " pdb=" C7 NAG a 1 " ideal model delta sigma weight residual 124.56 134.41 -9.85 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C2 NAG a 2 " pdb=" N2 NAG a 2 " pdb=" C7 NAG a 2 " ideal model delta sigma weight residual 124.56 134.03 -9.47 3.00e+00 1.11e-01 9.96e+00 angle pdb=" C2 NAG Q 2 " pdb=" N2 NAG Q 2 " pdb=" C7 NAG Q 2 " ideal model delta sigma weight residual 124.56 133.99 -9.43 3.00e+00 1.11e-01 9.89e+00 ... (remaining 26077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.90: 11778 23.90 - 47.80: 422 47.80 - 71.70: 92 71.70 - 95.60: 19 95.60 - 119.50: 34 Dihedral angle restraints: 12345 sinusoidal: 5874 harmonic: 6471 Sorted by residual: dihedral pdb=" CB CYS A 227 " pdb=" SG CYS A 227 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual 93.00 -176.56 -90.44 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS C 227 " pdb=" SG CYS C 227 " pdb=" SG CYS C 246 " pdb=" CB CYS C 246 " ideal model delta sinusoidal sigma weight residual 93.00 179.56 -86.56 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS B 227 " pdb=" SG CYS B 227 " pdb=" SG CYS B 246 " pdb=" CB CYS B 246 " ideal model delta sinusoidal sigma weight residual -86.00 -163.51 77.51 1 1.00e+01 1.00e-02 7.52e+01 ... (remaining 12342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2562 0.055 - 0.109: 414 0.109 - 0.164: 79 0.164 - 0.219: 2 0.219 - 0.273: 6 Chirality restraints: 3063 Sorted by residual: chirality pdb=" C2 NAG V 1 " pdb=" C1 NAG V 1 " pdb=" C3 NAG V 1 " pdb=" N2 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.22 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C2 NAG Q 1 " pdb=" C1 NAG Q 1 " pdb=" C3 NAG Q 1 " pdb=" N2 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.22 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2 NAG a 1 " pdb=" C1 NAG a 1 " pdb=" C3 NAG a 1 " pdb=" N2 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.22 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3060 not shown) Planarity restraints: 3255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 441 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO B 442 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 442 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 442 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 441 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 442 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 442 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 442 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 446 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 447 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 447 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 447 " -0.019 5.00e-02 4.00e+02 ... (remaining 3252 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 241 2.67 - 3.23: 16210 3.23 - 3.78: 29177 3.78 - 4.34: 40980 4.34 - 4.90: 65445 Nonbonded interactions: 152053 Sorted by model distance: nonbonded pdb=" OD1 ASP F 584 " pdb=" OG1 THR F 587 " model vdw 2.112 3.040 nonbonded pdb=" OD1 ASP E 584 " pdb=" OG1 THR E 587 " model vdw 2.118 3.040 nonbonded pdb=" OD1 ASP D 584 " pdb=" OG1 THR D 587 " model vdw 2.157 3.040 nonbonded pdb=" O ILE C 351 " pdb=" OG SER C 373 " model vdw 2.249 3.040 nonbonded pdb=" O ILE B 351 " pdb=" OG SER B 373 " model vdw 2.273 3.040 ... (remaining 152048 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'R' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'd' selection = chain 'g' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.370 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.780 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.003 0.042 19233 Z= 0.112 Angle : 0.567 9.971 26361 Z= 0.271 Chirality : 0.044 0.273 3063 Planarity : 0.004 0.039 3225 Dihedral : 14.180 119.498 8100 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.15 % 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: 0.19 (0.18), residues: 2199 helix: 0.04 (0.28), residues: 315 sheet: 0.62 (0.21), residues: 699 loop : -0.06 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 539 TYR 0.017 0.001 TYR H 99 PHE 0.012 0.001 PHE I 108 TRP 0.016 0.002 TRP E 572 HIS 0.004 0.001 HIS K 37 Details of bonding type rmsd covalent geometry : bond 0.00252 (19131) covalent geometry : angle 0.54617 (26082) SS BOND : bond 0.00540 ( 27) SS BOND : angle 1.61477 ( 54) hydrogen bonds : bond 0.23892 ( 606) hydrogen bonds : angle 8.09972 ( 1710) link_ALPHA1-3 : bond 0.00521 ( 3) link_ALPHA1-3 : angle 1.40685 ( 9) link_ALPHA1-6 : bond 0.00483 ( 3) link_ALPHA1-6 : angle 1.37452 ( 9) link_BETA1-4 : bond 0.00389 ( 36) link_BETA1-4 : angle 1.55284 ( 108) link_BETA1-6 : bond 0.00419 ( 3) link_BETA1-6 : angle 0.94953 ( 9) link_NAG-ASN : bond 0.00197 ( 30) link_NAG-ASN : angle 1.70494 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: G 12 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7639 (mmmm) REVERT: G 13 LYS cc_start: 0.7517 (mmtt) cc_final: 0.7187 (tptp) REVERT: H 84 ASN cc_start: 0.8390 (m-40) cc_final: 0.7837 (m-40) REVERT: I 12 LYS cc_start: 0.8242 (mmtt) cc_final: 0.8010 (mmmm) REVERT: I 80 TYR cc_start: 0.8391 (m-80) cc_final: 0.8137 (m-80) REVERT: I 84 ASN cc_start: 0.8056 (m-40) cc_final: 0.7580 (m-40) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.6271 time to fit residues: 250.7612 Evaluate side-chains 276 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 571 HIS F 571 HIS G 6 GLN H 35 ASN I 6 GLN K 16 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.108880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.069085 restraints weight = 30187.004| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.00 r_work: 0.2824 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 19233 Z= 0.294 Angle : 0.739 10.196 26361 Z= 0.358 Chirality : 0.050 0.317 3063 Planarity : 0.005 0.049 3225 Dihedral : 9.564 111.540 3933 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.74 % Allowed : 10.92 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.15 % 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: 0.22 (0.18), residues: 2199 helix: 0.37 (0.29), residues: 318 sheet: 0.74 (0.20), residues: 696 loop : -0.21 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 530 TYR 0.024 0.002 TYR H 99 PHE 0.014 0.002 PHE E 500 TRP 0.024 0.002 TRP E 572 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00710 (19131) covalent geometry : angle 0.71461 (26082) SS BOND : bond 0.00644 ( 27) SS BOND : angle 1.86854 ( 54) hydrogen bonds : bond 0.05667 ( 606) hydrogen bonds : angle 6.03723 ( 1710) link_ALPHA1-3 : bond 0.00518 ( 3) link_ALPHA1-3 : angle 2.04079 ( 9) link_ALPHA1-6 : bond 0.00436 ( 3) link_ALPHA1-6 : angle 2.10991 ( 9) link_BETA1-4 : bond 0.00356 ( 36) link_BETA1-4 : angle 1.74309 ( 108) link_BETA1-6 : bond 0.00234 ( 3) link_BETA1-6 : angle 1.07322 ( 9) link_NAG-ASN : bond 0.00468 ( 30) link_NAG-ASN : angle 2.26571 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6701 (pp20) REVERT: B 244 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7493 (pp20) REVERT: C 244 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6664 (pp20) REVERT: C 286 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8478 (mp10) REVERT: C 301 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7767 (mppt) REVERT: D 521 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8464 (tttm) REVERT: D 567 GLU cc_start: 0.7703 (tp30) cc_final: 0.7472 (tp30) REVERT: E 506 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8962 (ttmt) REVERT: E 567 GLU cc_start: 0.7820 (tp30) cc_final: 0.7613 (tp30) REVERT: F 567 GLU cc_start: 0.7850 (tp30) cc_final: 0.7561 (tp30) REVERT: G 3 GLN cc_start: 0.8596 (pt0) cc_final: 0.8383 (pt0) REVERT: G 12 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7499 (mmmm) REVERT: G 25 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8036 (p) REVERT: I 12 LYS cc_start: 0.8448 (mmtt) cc_final: 0.7944 (mmmm) REVERT: I 100 TYR cc_start: 0.7459 (t80) cc_final: 0.7187 (t80) REVERT: J 45 GLN cc_start: 0.8284 (mt0) cc_final: 0.7812 (mt0) REVERT: J 58 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7900 (tm-30) REVERT: K 45 GLN cc_start: 0.8444 (mt0) cc_final: 0.8022 (mt0) REVERT: K 64 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6816 (ttp-110) REVERT: K 85 ASP cc_start: 0.6604 (m-30) cc_final: 0.6328 (m-30) REVERT: L 45 GLN cc_start: 0.8202 (mt0) cc_final: 0.7651 (mt0) outliers start: 34 outliers final: 13 residues processed: 299 average time/residue: 0.7093 time to fit residues: 235.6367 Evaluate side-chains 290 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain E residue 499 ASN Chi-restraints excluded: chain E residue 506 LYS Chi-restraints excluded: chain E residue 599 GLU Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 571 HIS F 571 HIS I 3 GLN K 16 GLN L 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.110328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.070857 restraints weight = 30611.965| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.03 r_work: 0.2827 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19233 Z= 0.138 Angle : 0.609 9.899 26361 Z= 0.293 Chirality : 0.045 0.260 3063 Planarity : 0.005 0.049 3225 Dihedral : 7.607 110.212 3933 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.62 % Allowed : 12.51 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.15 % 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: 0.52 (0.18), residues: 2199 helix: 1.14 (0.31), residues: 300 sheet: 0.85 (0.21), residues: 696 loop : -0.10 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 23 TYR 0.014 0.001 TYR G 99 PHE 0.010 0.001 PHE J 74 TRP 0.018 0.001 TRP E 572 HIS 0.004 0.001 HIS F 571 Details of bonding type rmsd covalent geometry : bond 0.00322 (19131) covalent geometry : angle 0.59154 (26082) SS BOND : bond 0.00288 ( 27) SS BOND : angle 1.12739 ( 54) hydrogen bonds : bond 0.04139 ( 606) hydrogen bonds : angle 5.37703 ( 1710) link_ALPHA1-3 : bond 0.00669 ( 3) link_ALPHA1-3 : angle 1.84875 ( 9) link_ALPHA1-6 : bond 0.00592 ( 3) link_ALPHA1-6 : angle 1.87887 ( 9) link_BETA1-4 : bond 0.00380 ( 36) link_BETA1-4 : angle 1.47595 ( 108) link_BETA1-6 : bond 0.00273 ( 3) link_BETA1-6 : angle 1.16166 ( 9) link_NAG-ASN : bond 0.00160 ( 30) link_NAG-ASN : angle 1.72350 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6751 (pp20) REVERT: B 244 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7574 (pp20) REVERT: B 301 LYS cc_start: 0.8396 (mppt) cc_final: 0.7962 (mttp) REVERT: C 244 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6700 (pp20) REVERT: C 314 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8758 (mm-30) REVERT: D 521 LYS cc_start: 0.8854 (ttmm) cc_final: 0.8432 (tttp) REVERT: G 3 GLN cc_start: 0.8546 (pt0) cc_final: 0.8345 (pt0) REVERT: G 12 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7603 (mmmm) REVERT: G 25 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.8129 (p) REVERT: G 67 ARG cc_start: 0.8098 (ptt-90) cc_final: 0.7631 (ptt-90) REVERT: H 12 LYS cc_start: 0.8452 (tptp) cc_final: 0.7858 (mmmm) REVERT: H 67 ARG cc_start: 0.8259 (ptt-90) cc_final: 0.7572 (ptt-90) REVERT: H 86 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6646 (mt) REVERT: I 12 LYS cc_start: 0.8480 (mmtt) cc_final: 0.7893 (mmmm) REVERT: I 67 ARG cc_start: 0.7897 (ptt-90) cc_final: 0.7502 (ptt-90) REVERT: I 82 GLN cc_start: 0.8626 (tp40) cc_final: 0.8348 (tp40) REVERT: I 100 TYR cc_start: 0.7421 (t80) cc_final: 0.7133 (t80) REVERT: J 23 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7831 (mmm-85) REVERT: J 45 GLN cc_start: 0.8275 (mt0) cc_final: 0.7711 (mt0) REVERT: J 58 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7806 (tm-30) REVERT: J 107 LEU cc_start: 0.7759 (tm) cc_final: 0.7405 (tt) REVERT: K 45 GLN cc_start: 0.8417 (mt0) cc_final: 0.8045 (mt0) REVERT: K 64 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6772 (ttp-110) REVERT: K 82 GLU cc_start: 0.6333 (mt-10) cc_final: 0.5826 (mt-10) REVERT: L 45 GLN cc_start: 0.8239 (mt0) cc_final: 0.7737 (mt0) outliers start: 51 outliers final: 21 residues processed: 317 average time/residue: 0.6389 time to fit residues: 225.5359 Evaluate side-chains 306 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 278 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain F residue 538 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 21 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN G 85 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.109580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.070005 restraints weight = 30767.169| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.04 r_work: 0.2845 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 19233 Z= 0.174 Angle : 0.643 10.025 26361 Z= 0.310 Chirality : 0.046 0.272 3063 Planarity : 0.005 0.047 3225 Dihedral : 7.264 105.186 3933 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.56 % Allowed : 13.18 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.18), residues: 2199 helix: 1.01 (0.30), residues: 318 sheet: 0.82 (0.21), residues: 699 loop : -0.13 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 17 TYR 0.016 0.001 TYR G 99 PHE 0.011 0.001 PHE E 500 TRP 0.020 0.002 TRP E 572 HIS 0.003 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00416 (19131) covalent geometry : angle 0.62082 (26082) SS BOND : bond 0.00327 ( 27) SS BOND : angle 1.89638 ( 54) hydrogen bonds : bond 0.04153 ( 606) hydrogen bonds : angle 5.36735 ( 1710) link_ALPHA1-3 : bond 0.00646 ( 3) link_ALPHA1-3 : angle 1.86896 ( 9) link_ALPHA1-6 : bond 0.00765 ( 3) link_ALPHA1-6 : angle 1.94641 ( 9) link_BETA1-4 : bond 0.00369 ( 36) link_BETA1-4 : angle 1.53274 ( 108) link_BETA1-6 : bond 0.00237 ( 3) link_BETA1-6 : angle 1.12125 ( 9) link_NAG-ASN : bond 0.00241 ( 30) link_NAG-ASN : angle 1.86712 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6797 (pp20) REVERT: B 101 TYR cc_start: 0.8809 (m-80) cc_final: 0.8578 (m-80) REVERT: B 141 CYS cc_start: 0.8926 (m) cc_final: 0.8651 (p) REVERT: B 244 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7633 (pp20) REVERT: B 301 LYS cc_start: 0.8435 (mppt) cc_final: 0.7864 (mptt) REVERT: B 454 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: C 244 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6792 (pp20) REVERT: D 521 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8420 (tttp) REVERT: G 3 GLN cc_start: 0.8555 (pt0) cc_final: 0.8340 (pt0) REVERT: G 12 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7596 (mmmm) REVERT: G 25 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8114 (p) REVERT: G 38 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8070 (tttp) REVERT: H 12 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7882 (mmmm) REVERT: H 67 ARG cc_start: 0.8200 (ptt-90) cc_final: 0.7643 (ptt-90) REVERT: H 82 GLN cc_start: 0.8375 (tp40) cc_final: 0.8014 (tp40) REVERT: I 12 LYS cc_start: 0.8517 (mmtt) cc_final: 0.7991 (mmmm) REVERT: I 38 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7758 (tttp) REVERT: I 100 TYR cc_start: 0.7399 (t80) cc_final: 0.7176 (t80) REVERT: J 45 GLN cc_start: 0.8302 (mt0) cc_final: 0.7775 (mt0) REVERT: J 58 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7866 (tm-30) REVERT: K 45 GLN cc_start: 0.8462 (mt0) cc_final: 0.8071 (mt0) REVERT: K 64 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6986 (ttp-110) REVERT: K 85 ASP cc_start: 0.6731 (m-30) cc_final: 0.6466 (m-30) REVERT: L 45 GLN cc_start: 0.8229 (mt0) cc_final: 0.7756 (mt0) outliers start: 50 outliers final: 23 residues processed: 308 average time/residue: 0.6346 time to fit residues: 217.0184 Evaluate side-chains 307 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 506 LYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 195 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 527 ASN G 85 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.069621 restraints weight = 30674.941| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.03 r_work: 0.2841 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 19233 Z= 0.188 Angle : 0.651 10.053 26361 Z= 0.313 Chirality : 0.046 0.276 3063 Planarity : 0.005 0.053 3225 Dihedral : 7.052 101.523 3933 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.56 % Allowed : 13.85 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.18), residues: 2199 helix: 1.05 (0.30), residues: 318 sheet: 0.82 (0.21), residues: 699 loop : -0.15 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 17 TYR 0.016 0.001 TYR G 99 PHE 0.013 0.001 PHE J 35 TRP 0.022 0.002 TRP E 572 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00451 (19131) covalent geometry : angle 0.63023 (26082) SS BOND : bond 0.00359 ( 27) SS BOND : angle 1.71532 ( 54) hydrogen bonds : bond 0.04218 ( 606) hydrogen bonds : angle 5.28511 ( 1710) link_ALPHA1-3 : bond 0.00679 ( 3) link_ALPHA1-3 : angle 1.91781 ( 9) link_ALPHA1-6 : bond 0.00974 ( 3) link_ALPHA1-6 : angle 2.11750 ( 9) link_BETA1-4 : bond 0.00362 ( 36) link_BETA1-4 : angle 1.54307 ( 108) link_BETA1-6 : bond 0.00216 ( 3) link_BETA1-6 : angle 1.13202 ( 9) link_NAG-ASN : bond 0.00250 ( 30) link_NAG-ASN : angle 1.90610 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6802 (pp20) REVERT: B 101 TYR cc_start: 0.8853 (m-80) cc_final: 0.8651 (m-80) REVERT: B 141 CYS cc_start: 0.8920 (m) cc_final: 0.8643 (p) REVERT: B 229 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8386 (mptt) REVERT: B 244 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7649 (pp20) REVERT: B 301 LYS cc_start: 0.8454 (mppt) cc_final: 0.8030 (mttt) REVERT: B 454 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: C 244 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6801 (pp20) REVERT: D 521 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8430 (tttp) REVERT: E 567 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7559 (tp30) REVERT: G 3 GLN cc_start: 0.8571 (pt0) cc_final: 0.8364 (pt0) REVERT: G 12 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7607 (mmmm) REVERT: G 25 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8149 (p) REVERT: G 38 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8078 (tttp) REVERT: G 100 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6944 (t80) REVERT: H 12 LYS cc_start: 0.8503 (tptp) cc_final: 0.7950 (mmmm) REVERT: H 67 ARG cc_start: 0.8179 (ptt-90) cc_final: 0.7741 (ptt-90) REVERT: H 82 GLN cc_start: 0.8432 (tp40) cc_final: 0.8128 (tp40) REVERT: I 12 LYS cc_start: 0.8531 (mmtt) cc_final: 0.7940 (mmmm) REVERT: I 38 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7771 (tttp) REVERT: J 23 ARG cc_start: 0.8417 (mmm160) cc_final: 0.8156 (mmm160) REVERT: J 45 GLN cc_start: 0.8319 (mt0) cc_final: 0.7837 (mt0) REVERT: J 58 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7912 (tm-30) REVERT: K 45 GLN cc_start: 0.8489 (mt0) cc_final: 0.8091 (mt0) REVERT: K 64 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7112 (ttp-110) REVERT: K 85 ASP cc_start: 0.6736 (m-30) cc_final: 0.6508 (m-30) REVERT: L 45 GLN cc_start: 0.8272 (mt0) cc_final: 0.7773 (mt0) outliers start: 50 outliers final: 29 residues processed: 302 average time/residue: 0.6483 time to fit residues: 217.3947 Evaluate side-chains 310 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 506 LYS Chi-restraints excluded: chain F residue 583 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 166 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 119 optimal weight: 0.0870 chunk 192 optimal weight: 0.0470 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 135 optimal weight: 1.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 527 ASN G 6 GLN G 85 ASN ** I 3 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 = 0.3698 r_free = 0.3698 target = 0.110567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.070849 restraints weight = 30535.244| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.05 r_work: 0.2877 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19233 Z= 0.106 Angle : 0.600 9.834 26361 Z= 0.286 Chirality : 0.044 0.250 3063 Planarity : 0.004 0.051 3225 Dihedral : 6.685 96.794 3933 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.10 % Allowed : 14.97 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 2199 helix: 1.58 (0.32), residues: 300 sheet: 0.92 (0.21), residues: 696 loop : -0.04 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 17 TYR 0.010 0.001 TYR G 99 PHE 0.008 0.001 PHE D 500 TRP 0.017 0.001 TRP D 572 HIS 0.002 0.001 HIS F 604 Details of bonding type rmsd covalent geometry : bond 0.00243 (19131) covalent geometry : angle 0.58326 (26082) SS BOND : bond 0.00192 ( 27) SS BOND : angle 1.21863 ( 54) hydrogen bonds : bond 0.03307 ( 606) hydrogen bonds : angle 4.99944 ( 1710) link_ALPHA1-3 : bond 0.00797 ( 3) link_ALPHA1-3 : angle 1.89967 ( 9) link_ALPHA1-6 : bond 0.01322 ( 3) link_ALPHA1-6 : angle 2.20616 ( 9) link_BETA1-4 : bond 0.00399 ( 36) link_BETA1-4 : angle 1.41503 ( 108) link_BETA1-6 : bond 0.00251 ( 3) link_BETA1-6 : angle 1.20741 ( 9) link_NAG-ASN : bond 0.00136 ( 30) link_NAG-ASN : angle 1.55719 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6773 (pp20) REVERT: B 101 TYR cc_start: 0.8853 (m-80) cc_final: 0.8618 (m-80) REVERT: B 141 CYS cc_start: 0.8934 (m) cc_final: 0.8641 (p) REVERT: B 244 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7608 (pp20) REVERT: B 301 LYS cc_start: 0.8465 (mppt) cc_final: 0.7926 (mptt) REVERT: B 454 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: C 244 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6836 (pp20) REVERT: C 314 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8702 (mm-30) REVERT: D 521 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8352 (tttp) REVERT: D 567 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7567 (tp30) REVERT: E 567 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7545 (tp30) REVERT: G 12 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7622 (mmmm) REVERT: G 25 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8225 (p) REVERT: G 38 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8077 (tttp) REVERT: G 67 ARG cc_start: 0.7915 (ptt-90) cc_final: 0.7504 (ptt-90) REVERT: G 100 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6982 (t80) REVERT: H 12 LYS cc_start: 0.8533 (tptp) cc_final: 0.8021 (mmmm) REVERT: H 23 LYS cc_start: 0.8734 (tttp) cc_final: 0.8424 (tmtm) REVERT: H 67 ARG cc_start: 0.8228 (ptt-90) cc_final: 0.7694 (ptt-90) REVERT: H 82 GLN cc_start: 0.8477 (tp40) cc_final: 0.8265 (tp40) REVERT: I 12 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8043 (mmmm) REVERT: I 19 LYS cc_start: 0.8633 (tppt) cc_final: 0.8285 (tppt) REVERT: I 38 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7781 (tttp) REVERT: I 67 ARG cc_start: 0.7721 (ptt-90) cc_final: 0.7429 (ptt-90) REVERT: J 23 ARG cc_start: 0.8440 (mmm160) cc_final: 0.8154 (mmm160) REVERT: J 36 MET cc_start: 0.9189 (tpp) cc_final: 0.8957 (tpt) REVERT: J 45 GLN cc_start: 0.8269 (mt0) cc_final: 0.7844 (mt0) REVERT: J 58 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7888 (tm-30) REVERT: K 45 GLN cc_start: 0.8422 (mt0) cc_final: 0.8034 (mt0) REVERT: K 64 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7064 (ttp-110) REVERT: K 82 GLU cc_start: 0.6408 (mt-10) cc_final: 0.6099 (mt-10) REVERT: L 23 ARG cc_start: 0.8308 (mmm160) cc_final: 0.7937 (mmm160) REVERT: L 45 GLN cc_start: 0.8252 (mt0) cc_final: 0.7759 (mt0) REVERT: L 64 ARG cc_start: 0.7519 (mtm110) cc_final: 0.7234 (mtm-85) REVERT: L 107 LEU cc_start: 0.7373 (tm) cc_final: 0.7093 (tt) outliers start: 41 outliers final: 19 residues processed: 305 average time/residue: 0.6726 time to fit residues: 228.0072 Evaluate side-chains 307 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 278 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 506 LYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 29 optimal weight: 0.3980 chunk 168 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 ASN B 421 GLN E 527 ASN G 3 GLN G 85 ASN ** I 3 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 = 0.3677 r_free = 0.3677 target = 0.109083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.069005 restraints weight = 30762.551| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.06 r_work: 0.2839 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 19233 Z= 0.178 Angle : 0.646 10.029 26361 Z= 0.309 Chirality : 0.046 0.275 3063 Planarity : 0.005 0.056 3225 Dihedral : 6.645 92.240 3933 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.21 % Allowed : 15.59 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.18), residues: 2199 helix: 1.24 (0.31), residues: 318 sheet: 1.16 (0.21), residues: 672 loop : -0.20 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 17 TYR 0.014 0.001 TYR G 99 PHE 0.013 0.001 PHE J 35 TRP 0.021 0.002 TRP E 572 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00426 (19131) covalent geometry : angle 0.62633 (26082) SS BOND : bond 0.00300 ( 27) SS BOND : angle 1.51237 ( 54) hydrogen bonds : bond 0.03977 ( 606) hydrogen bonds : angle 5.10138 ( 1710) link_ALPHA1-3 : bond 0.00771 ( 3) link_ALPHA1-3 : angle 2.02299 ( 9) link_ALPHA1-6 : bond 0.01359 ( 3) link_ALPHA1-6 : angle 2.34384 ( 9) link_BETA1-4 : bond 0.00371 ( 36) link_BETA1-4 : angle 1.53099 ( 108) link_BETA1-6 : bond 0.00273 ( 3) link_BETA1-6 : angle 1.10071 ( 9) link_NAG-ASN : bond 0.00231 ( 30) link_NAG-ASN : angle 1.84174 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6767 (pp20) REVERT: B 101 TYR cc_start: 0.8885 (m-80) cc_final: 0.8642 (m-80) REVERT: B 141 CYS cc_start: 0.8936 (m) cc_final: 0.8635 (p) REVERT: B 229 LYS cc_start: 0.8547 (mmtm) cc_final: 0.8310 (mptt) REVERT: B 244 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7644 (pp20) REVERT: B 301 LYS cc_start: 0.8453 (mppt) cc_final: 0.7963 (mppt) REVERT: B 454 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: C 244 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6830 (pp20) REVERT: D 521 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8397 (tttp) REVERT: D 567 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7519 (tp30) REVERT: E 567 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7542 (tp30) REVERT: F 567 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7570 (tp30) REVERT: G 3 GLN cc_start: 0.8548 (pt0) cc_final: 0.8342 (pt0) REVERT: G 12 LYS cc_start: 0.8427 (mmtt) cc_final: 0.7683 (mmmm) REVERT: G 25 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8208 (p) REVERT: G 38 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8055 (tttp) REVERT: G 67 ARG cc_start: 0.7909 (ptt-90) cc_final: 0.7463 (ptt-90) REVERT: G 100 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6976 (t80) REVERT: H 12 LYS cc_start: 0.8524 (tptp) cc_final: 0.8035 (mmmm) REVERT: H 23 LYS cc_start: 0.8716 (tttp) cc_final: 0.8393 (tmtm) REVERT: H 67 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7561 (ptt-90) REVERT: H 82 GLN cc_start: 0.8492 (tp40) cc_final: 0.8208 (tp40) REVERT: I 12 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8089 (mmmm) REVERT: I 19 LYS cc_start: 0.8582 (tppt) cc_final: 0.8257 (tppt) REVERT: J 23 ARG cc_start: 0.8446 (mmm160) cc_final: 0.8119 (mmm160) REVERT: J 36 MET cc_start: 0.9194 (tpp) cc_final: 0.8928 (tpt) REVERT: J 45 GLN cc_start: 0.8302 (mt0) cc_final: 0.7727 (mt0) REVERT: J 58 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7948 (tm-30) REVERT: K 45 GLN cc_start: 0.8454 (mt0) cc_final: 0.8044 (mt0) REVERT: K 64 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7068 (ttp-110) REVERT: K 85 ASP cc_start: 0.6562 (m-30) cc_final: 0.6354 (m-30) REVERT: L 23 ARG cc_start: 0.8317 (mmm160) cc_final: 0.7932 (mmm160) REVERT: L 45 GLN cc_start: 0.8259 (mt0) cc_final: 0.7742 (mt0) REVERT: L 107 LEU cc_start: 0.7375 (tm) cc_final: 0.7102 (tt) outliers start: 43 outliers final: 22 residues processed: 303 average time/residue: 0.7118 time to fit residues: 239.6263 Evaluate side-chains 307 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 276 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 408 CYS Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 506 LYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 110 optimal weight: 4.9990 chunk 121 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 ASN B 421 GLN E 527 ASN G 85 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.109629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069706 restraints weight = 30573.240| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.05 r_work: 0.2855 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19233 Z= 0.140 Angle : 0.628 9.927 26361 Z= 0.299 Chirality : 0.045 0.263 3063 Planarity : 0.005 0.055 3225 Dihedral : 6.497 87.015 3933 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.41 % Allowed : 15.38 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.18), residues: 2199 helix: 1.58 (0.32), residues: 300 sheet: 1.19 (0.21), residues: 672 loop : -0.15 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 17 TYR 0.012 0.001 TYR G 99 PHE 0.010 0.001 PHE D 500 TRP 0.019 0.001 TRP E 572 HIS 0.003 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00334 (19131) covalent geometry : angle 0.60982 (26082) SS BOND : bond 0.00233 ( 27) SS BOND : angle 1.29388 ( 54) hydrogen bonds : bond 0.03646 ( 606) hydrogen bonds : angle 5.00363 ( 1710) link_ALPHA1-3 : bond 0.00873 ( 3) link_ALPHA1-3 : angle 2.06022 ( 9) link_ALPHA1-6 : bond 0.01594 ( 3) link_ALPHA1-6 : angle 2.44749 ( 9) link_BETA1-4 : bond 0.00371 ( 36) link_BETA1-4 : angle 1.47657 ( 108) link_BETA1-6 : bond 0.00250 ( 3) link_BETA1-6 : angle 1.15527 ( 9) link_NAG-ASN : bond 0.00160 ( 30) link_NAG-ASN : angle 1.70002 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 279 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6776 (pp20) REVERT: B 101 TYR cc_start: 0.8884 (m-80) cc_final: 0.8629 (m-80) REVERT: B 141 CYS cc_start: 0.8940 (m) cc_final: 0.8634 (p) REVERT: B 229 LYS cc_start: 0.8548 (mmtm) cc_final: 0.8318 (mptt) REVERT: B 244 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7633 (pp20) REVERT: B 301 LYS cc_start: 0.8451 (mppt) cc_final: 0.7962 (mppt) REVERT: B 454 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: C 244 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6823 (pp20) REVERT: C 314 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8711 (mm-30) REVERT: D 521 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8406 (tttp) REVERT: D 567 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7487 (tp30) REVERT: E 567 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7510 (tp30) REVERT: F 567 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7532 (tp30) REVERT: G 3 GLN cc_start: 0.8544 (pt0) cc_final: 0.8343 (pt0) REVERT: G 12 LYS cc_start: 0.8425 (mmtt) cc_final: 0.7714 (mmmm) REVERT: G 25 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8236 (p) REVERT: G 38 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8070 (tttp) REVERT: G 67 ARG cc_start: 0.7830 (ptt-90) cc_final: 0.7221 (ptt-90) REVERT: G 100 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6969 (t80) REVERT: H 12 LYS cc_start: 0.8519 (tptp) cc_final: 0.7995 (mmmm) REVERT: H 23 LYS cc_start: 0.8759 (tttp) cc_final: 0.8395 (tmtm) REVERT: H 67 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7538 (ptt-90) REVERT: H 82 GLN cc_start: 0.8529 (tp40) cc_final: 0.8227 (tp40) REVERT: I 12 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8149 (mmmm) REVERT: I 19 LYS cc_start: 0.8590 (tppt) cc_final: 0.8293 (tppt) REVERT: J 23 ARG cc_start: 0.8474 (mmm160) cc_final: 0.8131 (mmm160) REVERT: J 36 MET cc_start: 0.9157 (tpp) cc_final: 0.8897 (tpt) REVERT: J 45 GLN cc_start: 0.8284 (mt0) cc_final: 0.7709 (mt0) REVERT: J 58 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7896 (tm-30) REVERT: K 45 GLN cc_start: 0.8407 (mt0) cc_final: 0.7993 (mt0) REVERT: K 64 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7030 (ttp-110) REVERT: K 82 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6319 (mt-10) REVERT: K 85 ASP cc_start: 0.6590 (m-30) cc_final: 0.6331 (m-30) REVERT: L 23 ARG cc_start: 0.8284 (mmm160) cc_final: 0.7885 (mmm160) REVERT: L 45 GLN cc_start: 0.8282 (mt0) cc_final: 0.7779 (mt0) REVERT: L 64 ARG cc_start: 0.7557 (mtm110) cc_final: 0.7312 (mtm-85) outliers start: 47 outliers final: 26 residues processed: 308 average time/residue: 0.6813 time to fit residues: 233.0164 Evaluate side-chains 311 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 408 CYS Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 506 LYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 54 optimal weight: 0.0170 chunk 10 optimal weight: 0.6980 chunk 188 optimal weight: 10.0000 chunk 64 optimal weight: 0.0070 chunk 179 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 GLN E 527 ASN G 85 ASN ** I 3 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 = 0.3719 r_free = 0.3719 target = 0.111036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.072085 restraints weight = 30473.098| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.03 r_work: 0.2846 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19233 Z= 0.109 Angle : 0.609 9.834 26361 Z= 0.289 Chirality : 0.044 0.251 3063 Planarity : 0.004 0.055 3225 Dihedral : 6.250 76.936 3933 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.79 % Allowed : 16.10 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.18), residues: 2199 helix: 1.31 (0.31), residues: 318 sheet: 1.13 (0.20), residues: 708 loop : -0.08 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 17 TYR 0.011 0.001 TYR G 99 PHE 0.010 0.001 PHE G 64 TRP 0.017 0.001 TRP D 572 HIS 0.002 0.001 HIS F 604 Details of bonding type rmsd covalent geometry : bond 0.00253 (19131) covalent geometry : angle 0.59265 (26082) SS BOND : bond 0.00218 ( 27) SS BOND : angle 1.15209 ( 54) hydrogen bonds : bond 0.03233 ( 606) hydrogen bonds : angle 4.83699 ( 1710) link_ALPHA1-3 : bond 0.00967 ( 3) link_ALPHA1-3 : angle 2.07491 ( 9) link_ALPHA1-6 : bond 0.01806 ( 3) link_ALPHA1-6 : angle 2.60308 ( 9) link_BETA1-4 : bond 0.00398 ( 36) link_BETA1-4 : angle 1.41886 ( 108) link_BETA1-6 : bond 0.00295 ( 3) link_BETA1-6 : angle 1.17508 ( 9) link_NAG-ASN : bond 0.00126 ( 30) link_NAG-ASN : angle 1.48849 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6747 (pp20) REVERT: B 101 TYR cc_start: 0.8869 (m-80) cc_final: 0.8624 (m-80) REVERT: B 141 CYS cc_start: 0.8956 (m) cc_final: 0.8643 (p) REVERT: B 229 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8300 (mptt) REVERT: B 244 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7602 (pp20) REVERT: B 301 LYS cc_start: 0.8498 (mppt) cc_final: 0.7966 (mptt) REVERT: B 454 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: C 244 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6730 (pp20) REVERT: C 314 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8681 (mm-30) REVERT: D 521 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8344 (tttp) REVERT: D 567 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7452 (tp30) REVERT: E 567 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7571 (tp30) REVERT: F 567 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7477 (tp30) REVERT: G 12 LYS cc_start: 0.8432 (mmtt) cc_final: 0.7715 (mmmm) REVERT: G 38 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8039 (tttp) REVERT: G 67 ARG cc_start: 0.7641 (ptt-90) cc_final: 0.7233 (ptt-90) REVERT: G 100 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.7001 (t80) REVERT: H 12 LYS cc_start: 0.8474 (tptp) cc_final: 0.7946 (mmmm) REVERT: H 23 LYS cc_start: 0.8742 (tttp) cc_final: 0.8418 (tppp) REVERT: H 82 GLN cc_start: 0.8532 (tp40) cc_final: 0.8243 (tp40) REVERT: I 12 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8155 (mmmm) REVERT: I 19 LYS cc_start: 0.8537 (tppt) cc_final: 0.8277 (tppt) REVERT: J 17 ARG cc_start: 0.7899 (ttm110) cc_final: 0.6799 (ttm-80) REVERT: J 23 ARG cc_start: 0.8451 (mmm160) cc_final: 0.8093 (mmm160) REVERT: J 36 MET cc_start: 0.9127 (tpp) cc_final: 0.8858 (tpt) REVERT: J 45 GLN cc_start: 0.8208 (mt0) cc_final: 0.7688 (mt0) REVERT: J 58 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7884 (tm-30) REVERT: J 64 ARG cc_start: 0.7964 (ptp90) cc_final: 0.7633 (ttp80) REVERT: J 93 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8179 (tm-30) REVERT: K 45 GLN cc_start: 0.8347 (mt0) cc_final: 0.8035 (mt0) REVERT: K 64 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6934 (ttp-110) REVERT: K 73 ASP cc_start: 0.7740 (t0) cc_final: 0.7385 (m-30) REVERT: K 85 ASP cc_start: 0.6615 (m-30) cc_final: 0.6362 (m-30) REVERT: L 23 ARG cc_start: 0.8345 (mmm160) cc_final: 0.7937 (mmm160) REVERT: L 45 GLN cc_start: 0.8264 (mt0) cc_final: 0.7773 (mt0) REVERT: L 64 ARG cc_start: 0.7578 (mtm110) cc_final: 0.7291 (mtm-85) outliers start: 35 outliers final: 20 residues processed: 306 average time/residue: 0.7238 time to fit residues: 245.6384 Evaluate side-chains 308 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 408 CYS Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 506 LYS Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 164 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 GLN E 527 ASN G 3 GLN G 85 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.070609 restraints weight = 30533.478| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.04 r_work: 0.2841 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 19233 Z= 0.169 Angle : 0.772 59.186 26361 Z= 0.414 Chirality : 0.046 0.601 3063 Planarity : 0.005 0.067 3225 Dihedral : 6.258 77.548 3933 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 1.69 % Allowed : 16.26 % Favored : 82.05 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.18), residues: 2199 helix: 1.31 (0.31), residues: 318 sheet: 1.12 (0.20), residues: 708 loop : -0.08 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 17 TYR 0.010 0.001 TYR G 99 PHE 0.018 0.001 PHE G 64 TRP 0.017 0.001 TRP D 572 HIS 0.002 0.001 HIS F 604 Details of bonding type rmsd covalent geometry : bond 0.00368 (19131) covalent geometry : angle 0.75468 (26082) SS BOND : bond 0.00960 ( 27) SS BOND : angle 2.44062 ( 54) hydrogen bonds : bond 0.03290 ( 606) hydrogen bonds : angle 4.83558 ( 1710) link_ALPHA1-3 : bond 0.01198 ( 3) link_ALPHA1-3 : angle 2.22390 ( 9) link_ALPHA1-6 : bond 0.01624 ( 3) link_ALPHA1-6 : angle 2.59278 ( 9) link_BETA1-4 : bond 0.00386 ( 36) link_BETA1-4 : angle 1.42027 ( 108) link_BETA1-6 : bond 0.00196 ( 3) link_BETA1-6 : angle 1.12574 ( 9) link_NAG-ASN : bond 0.00134 ( 30) link_NAG-ASN : angle 1.46799 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6736 (pp20) REVERT: B 101 TYR cc_start: 0.8873 (m-80) cc_final: 0.8620 (m-80) REVERT: B 141 CYS cc_start: 0.8973 (m) cc_final: 0.8644 (p) REVERT: B 229 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8295 (mptt) REVERT: B 244 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7609 (pp20) REVERT: B 301 LYS cc_start: 0.8502 (mppt) cc_final: 0.7967 (mptt) REVERT: B 454 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: C 244 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6731 (pp20) REVERT: C 314 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8691 (mm-30) REVERT: D 521 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8342 (tttp) REVERT: D 567 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7458 (tp30) REVERT: E 567 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7578 (tp30) REVERT: F 567 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7529 (tp30) REVERT: G 12 LYS cc_start: 0.8428 (mmtt) cc_final: 0.7708 (mmmm) REVERT: G 38 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8025 (tttp) REVERT: G 67 ARG cc_start: 0.7691 (ptt-90) cc_final: 0.7096 (ptt-90) REVERT: G 85 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.7102 (p0) REVERT: G 100 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6893 (t80) REVERT: H 12 LYS cc_start: 0.8475 (tptp) cc_final: 0.7947 (mmmm) REVERT: H 23 LYS cc_start: 0.8735 (tttp) cc_final: 0.8416 (tppp) REVERT: H 82 GLN cc_start: 0.8529 (tp40) cc_final: 0.8236 (tp40) REVERT: I 12 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8144 (mmmm) REVERT: I 19 LYS cc_start: 0.8527 (tppt) cc_final: 0.8267 (tppt) REVERT: J 17 ARG cc_start: 0.7884 (ttm110) cc_final: 0.6808 (ttm-80) REVERT: J 23 ARG cc_start: 0.8457 (mmm160) cc_final: 0.8097 (mmm160) REVERT: J 36 MET cc_start: 0.9121 (tpp) cc_final: 0.8849 (tpt) REVERT: J 45 GLN cc_start: 0.8206 (mt0) cc_final: 0.7682 (mt0) REVERT: J 58 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7871 (tm-30) REVERT: J 64 ARG cc_start: 0.7965 (ptp90) cc_final: 0.7623 (ttp80) REVERT: J 93 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: K 45 GLN cc_start: 0.8347 (mt0) cc_final: 0.8033 (mt0) REVERT: K 64 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6932 (ttp-110) REVERT: K 85 ASP cc_start: 0.6594 (m-30) cc_final: 0.6353 (m-30) REVERT: L 23 ARG cc_start: 0.8323 (mmm160) cc_final: 0.7917 (mmm160) REVERT: L 45 GLN cc_start: 0.8247 (mt0) cc_final: 0.7741 (mt0) REVERT: L 64 ARG cc_start: 0.7568 (mtm110) cc_final: 0.7289 (mtm-85) outliers start: 33 outliers final: 23 residues processed: 299 average time/residue: 0.7232 time to fit residues: 239.9286 Evaluate side-chains 312 residues out of total 1956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 408 CYS Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 506 LYS Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 150 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 179 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 GLN E 527 ASN G 3 GLN ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 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 = 0.3717 r_free = 0.3717 target = 0.110883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071965 restraints weight = 30725.004| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.03 r_work: 0.2842 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.317 19233 Z= 0.200 Angle : 0.761 47.310 26361 Z= 0.467 Chirality : 0.047 0.684 3063 Planarity : 0.005 0.078 3225 Dihedral : 6.258 77.532 3933 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 1.64 % Allowed : 16.26 % Favored : 82.10 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.18), residues: 2199 helix: 1.31 (0.31), residues: 318 sheet: 1.12 (0.20), residues: 708 loop : -0.08 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 17 TYR 0.010 0.001 TYR G 99 PHE 0.018 0.001 PHE G 64 TRP 0.017 0.001 TRP D 572 HIS 0.002 0.001 HIS F 604 Details of bonding type rmsd covalent geometry : bond 0.00427 (19131) covalent geometry : angle 0.74375 (26082) SS BOND : bond 0.00959 ( 27) SS BOND : angle 2.44019 ( 54) hydrogen bonds : bond 0.03290 ( 606) hydrogen bonds : angle 4.83558 ( 1710) link_ALPHA1-3 : bond 0.01192 ( 3) link_ALPHA1-3 : angle 2.22031 ( 9) link_ALPHA1-6 : bond 0.01627 ( 3) link_ALPHA1-6 : angle 2.59398 ( 9) link_BETA1-4 : bond 0.00386 ( 36) link_BETA1-4 : angle 1.42036 ( 108) link_BETA1-6 : bond 0.00198 ( 3) link_BETA1-6 : angle 1.12668 ( 9) link_NAG-ASN : bond 0.00134 ( 30) link_NAG-ASN : angle 1.46799 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10438.79 seconds wall clock time: 177 minutes 48.45 seconds (10668.45 seconds total)