Starting phenix.real_space_refine on Tue May 20 17:40:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g85_29836/05_2025/8g85_29836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g85_29836/05_2025/8g85_29836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g85_29836/05_2025/8g85_29836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g85_29836/05_2025/8g85_29836.map" model { file = "/net/cci-nas-00/data/ceres_data/8g85_29836/05_2025/8g85_29836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g85_29836/05_2025/8g85_29836.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.010 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12577 2.51 5 N 3347 2.21 5 O 4037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20090 Number of models: 1 Model: "" Number of chains: 39 Chain: "G" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "D" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "J" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "K" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 831 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "C" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 831 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 831 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} 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: "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: 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: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "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: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "K" 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: 13.23, per 1000 atoms: 0.66 Number of scatterers: 20090 At special positions: 0 Unit cell: (132.016, 145.969, 140.602, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 4037 8.00 N 3347 7.00 C 12577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.05 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.04 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 433 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.03 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN M 4 " - " MAN M 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 5 " " BMA V 3 " - " MAN V 4 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 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 f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " 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-ASN " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG D 601 " - " ASN D 133 " " NAG D 602 " - " ASN D 156 " " NAG D 603 " - " ASN D 160 " " NAG D 604 " - " ASN D 197 " " NAG D 605 " - " ASN D 276 " " NAG D 606 " - " ASN D 301 " " NAG D 607 " - " ASN D 355 " " NAG D 608 " - " ASN D 339 " " NAG D 609 " - " ASN D 392 " " NAG D 610 " - " ASN D 234 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 156 " " NAG G 603 " - " ASN G 160 " " NAG G 604 " - " ASN G 197 " " NAG G 605 " - " ASN G 276 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 355 " " NAG G 608 " - " ASN G 339 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 234 " " NAG J 601 " - " ASN J 133 " " NAG J 602 " - " ASN J 156 " " NAG J 603 " - " ASN J 160 " " NAG J 604 " - " ASN J 197 " " NAG J 605 " - " ASN J 276 " " NAG J 606 " - " ASN J 301 " " NAG J 607 " - " ASN J 355 " " NAG J 608 " - " ASN J 339 " " NAG J 609 " - " ASN J 392 " " NAG J 610 " - " ASN J 234 " " NAG K 701 " - " ASN K 637 " " NAG M 1 " - " ASN G 262 " " NAG O 1 " - " ASN G 295 " " NAG P 1 " - " ASN G 332 " " NAG Q 1 " - " ASN G 363 " " NAG R 1 " - " ASN G 386 " " NAG S 1 " - " ASN G 448 " " NAG T 1 " - " ASN G 88 " " NAG U 1 " - " ASN D 88 " " NAG V 1 " - " ASN D 262 " " NAG X 1 " - " ASN D 295 " " NAG Y 1 " - " ASN D 332 " " NAG Z 1 " - " ASN D 363 " " NAG a 1 " - " ASN D 386 " " NAG b 1 " - " ASN D 448 " " NAG c 1 " - " ASN J 88 " " NAG d 1 " - " ASN J 262 " " NAG e 1 " - " ASN J 295 " " NAG f 1 " - " ASN J 332 " " NAG g 1 " - " ASN J 363 " " NAG h 1 " - " ASN J 386 " " NAG i 1 " - " ASN J 448 " Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.9 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 42 sheets defined 19.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.504A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER G 110 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.681A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 334 through 350 removed outlier: 3.794A pdb=" N GLN G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.820A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 removed outlier: 4.104A pdb=" N LEU G 390 " --> pdb=" O THR G 387 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE G 391 " --> pdb=" O SER G 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 387 through 391' Processing helix chain 'G' and resid 474 through 479 removed outlier: 3.761A pdb=" N ASP G 477 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.788A pdb=" N ALA B 517 " --> pdb=" O GLY B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 3.818A pdb=" N ALA B 526 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 527' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.699A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.945A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 removed outlier: 4.168A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 638 through 662 removed outlier: 4.060A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 115 removed outlier: 4.274A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.558A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 127 " --> pdb=" O PRO D 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 127' Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.570A pdb=" N MET D 150 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 350 removed outlier: 3.543A pdb=" N LYS D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.887A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 481 removed outlier: 4.045A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 517 Processing helix chain 'E' and resid 531 through 535 removed outlier: 4.105A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 542 removed outlier: 4.070A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 541 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 536 through 542' Processing helix chain 'E' and resid 572 through 596 removed outlier: 3.913A pdb=" N TYR E 586 " --> pdb=" O ALA E 582 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 593 " --> pdb=" O ASP E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 622 removed outlier: 3.517A pdb=" N ILE E 622 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 636 removed outlier: 4.087A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 662 removed outlier: 3.679A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 646 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN E 651 " --> pdb=" O GLU E 647 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS E 655 " --> pdb=" O ASN E 651 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 660 " --> pdb=" O ASN E 656 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 115 removed outlier: 4.102A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE J 109 " --> pdb=" O HIS J 105 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER J 115 " --> pdb=" O LEU J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 127 removed outlier: 3.759A pdb=" N CYS J 126 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL J 127 " --> pdb=" O PRO J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 353 removed outlier: 3.977A pdb=" N LYS J 347 " --> pdb=" O GLY J 343 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN J 348 " --> pdb=" O LYS J 344 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS J 351 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS J 352 " --> pdb=" O GLN J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.787A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 381 removed outlier: 4.135A pdb=" N GLY J 380 " --> pdb=" O ASN J 377 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU J 381 " --> pdb=" O CYS J 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 377 through 381' Processing helix chain 'J' and resid 474 through 482 removed outlier: 3.561A pdb=" N TRP J 479 " --> pdb=" O ARG J 476 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG J 480 " --> pdb=" O ASP J 477 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER J 481 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 517 removed outlier: 3.699A pdb=" N ALA K 517 " --> pdb=" O GLY K 514 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 534 Processing helix chain 'K' and resid 575 through 596 removed outlier: 3.502A pdb=" N LEU K 592 " --> pdb=" O ARG K 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 635 removed outlier: 3.533A pdb=" N TRP K 631 " --> pdb=" O THR K 627 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS K 633 " --> pdb=" O LEU K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 662 removed outlier: 3.689A pdb=" N ILE K 642 " --> pdb=" O TYR K 638 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY K 644 " --> pdb=" O GLN K 640 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU K 646 " --> pdb=" O ILE K 642 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU K 647 " --> pdb=" O TYR K 643 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU K 648 " --> pdb=" O GLY K 644 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN K 652 " --> pdb=" O GLU K 648 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.524A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'G' and resid 494 through 499 removed outlier: 3.551A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.899A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.835A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'G' and resid 181 through 182 Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.621A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE G 383 " --> pdb=" O PHE G 376 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.621A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.186A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.910A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 494 through 495 Processing sheet with id=AB1, first strand: chain 'D' and resid 494 through 495 Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.918A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 75 through 76 removed outlier: 4.339A pdb=" N VAL D 75 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 56 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.547A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.690A pdb=" N VAL D 172 " --> pdb=" O PHE D 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AB7, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.337A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL D 333 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE D 383 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE D 376 " --> pdb=" O PHE D 383 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.503A pdb=" N LEU D 285 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER D 393 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.843A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 494 through 499 removed outlier: 4.979A pdb=" N VAL J 36 " --> pdb=" O THR K 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 45 through 46 removed outlier: 3.787A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'J' and resid 130 through 133 Processing sheet with id=AC5, first strand: chain 'J' and resid 181 through 182 Processing sheet with id=AC6, first strand: chain 'J' and resid 259 through 261 removed outlier: 6.172A pdb=" N LEU J 260 " --> pdb=" O THR J 450 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N VAL J 442 " --> pdb=" O CYS J 296 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N CYS J 296 " --> pdb=" O VAL J 442 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N VAL J 292 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ASN J 448 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR J 450 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS J 330 " --> pdb=" O THR J 297 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL J 333 " --> pdb=" O ILE J 414 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE J 376 " --> pdb=" O PHE J 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 271 through 273 removed outlier: 3.934A pdb=" N MET J 271 " --> pdb=" O GLN J 287 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN J 287 " --> pdb=" O MET J 271 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 285 " --> pdb=" O ARG J 273 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR J 450 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ASN J 448 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N VAL J 292 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N CYS J 296 " --> pdb=" O VAL J 442 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N VAL J 442 " --> pdb=" O CYS J 296 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER J 393 " --> pdb=" O PHE J 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 305 through 312 removed outlier: 6.840A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 423 through 425 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.563A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER H 68 " --> pdb=" O LYS H 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.674A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA H 88 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU H 95 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR H 34 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP H 35 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.674A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA H 88 " --> pdb=" O LEU H 109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.504A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.336A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.553A pdb=" N PHE A 78 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.702A pdb=" N LEU A 109 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 88 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP A 35 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR A 50 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 48 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 38 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 58 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.702A pdb=" N LEU A 109 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 88 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AE1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.553A pdb=" N MET C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 49 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.652A pdb=" N VAL F 12 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA F 88 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP F 35 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR F 50 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS F 44 " --> pdb=" O PHE F 40 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY F 58 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.652A pdb=" N VAL F 12 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA F 88 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.616A pdb=" N MET I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR I 49 " --> pdb=" O THR I 53 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR I 53 " --> pdb=" O TYR I 49 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1485 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: 6.97 Time building geometry restraints manager: 6.49 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: 6274 1.34 - 1.47: 5131 1.47 - 1.59: 8916 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 20495 Sorted by residual: bond pdb=" C1 NAG D 610 " pdb=" O5 NAG D 610 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C1 NAG G 610 " pdb=" O5 NAG G 610 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 MAN M 5 " pdb=" C2 MAN M 5 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.46e+00 bond pdb=" C1 MAN M 5 " pdb=" O5 MAN M 5 " ideal model delta sigma weight residual 1.399 1.454 -0.055 2.00e-02 2.50e+03 7.46e+00 ... (remaining 20490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 27586 4.22 - 8.43: 225 8.43 - 12.65: 14 12.65 - 16.86: 3 16.86 - 21.08: 2 Bond angle restraints: 27830 Sorted by residual: angle pdb=" CG ARG H 94 " pdb=" CD ARG H 94 " pdb=" NE ARG H 94 " ideal model delta sigma weight residual 112.00 90.92 21.08 2.20e+00 2.07e-01 9.18e+01 angle pdb=" C ALA H 32 " pdb=" N TYR H 33 " pdb=" CA TYR H 33 " ideal model delta sigma weight residual 121.74 136.28 -14.54 1.58e+00 4.01e-01 8.47e+01 angle pdb=" CB ARG H 94 " pdb=" CG ARG H 94 " pdb=" CD ARG H 94 " ideal model delta sigma weight residual 111.30 128.66 -17.36 2.30e+00 1.89e-01 5.70e+01 angle pdb=" CA ARG H 94 " pdb=" CB ARG H 94 " pdb=" CG ARG H 94 " ideal model delta sigma weight residual 114.10 128.29 -14.19 2.00e+00 2.50e-01 5.03e+01 angle pdb=" C LYS H 64 " pdb=" CA LYS H 64 " pdb=" CB LYS H 64 " ideal model delta sigma weight residual 116.54 109.04 7.50 1.15e+00 7.56e-01 4.25e+01 ... (remaining 27825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 12508 24.04 - 48.07: 712 48.07 - 72.11: 146 72.11 - 96.15: 65 96.15 - 120.18: 50 Dihedral angle restraints: 13481 sinusoidal: 6593 harmonic: 6888 Sorted by residual: dihedral pdb=" CB CYS G 218 " pdb=" SG CYS G 218 " pdb=" SG CYS G 247 " pdb=" CB CYS G 247 " ideal model delta sinusoidal sigma weight residual -86.00 -5.65 -80.35 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -16.38 -69.62 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS J 54 " pdb=" SG CYS J 54 " pdb=" SG CYS J 74 " pdb=" CB CYS J 74 " ideal model delta sinusoidal sigma weight residual -86.00 -16.88 -69.12 1 1.00e+01 1.00e-02 6.18e+01 ... (remaining 13478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3035 0.095 - 0.190: 333 0.190 - 0.285: 20 0.285 - 0.380: 5 0.380 - 0.474: 2 Chirality restraints: 3395 Sorted by residual: chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 611 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" C1 NAG E 701 " pdb=" ND2 ASN E 611 " pdb=" C2 NAG E 701 " pdb=" O5 NAG E 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C1 NAG D 605 " pdb=" ND2 ASN D 276 " pdb=" C2 NAG D 605 " pdb=" O5 NAG D 605 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 3392 not shown) Planarity restraints: 3472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 94 " 0.096 9.50e-02 1.11e+02 5.47e-02 1.54e+01 pdb=" NE ARG F 94 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG F 94 " 0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG F 94 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG F 94 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 497 " -0.062 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO D 498 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO D 498 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 498 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 42 " 0.042 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO G 43 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO G 43 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 43 " 0.036 5.00e-02 4.00e+02 ... (remaining 3469 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4061 2.79 - 3.32: 16698 3.32 - 3.84: 31260 3.84 - 4.37: 34508 4.37 - 4.90: 60633 Nonbonded interactions: 147160 Sorted by model distance: nonbonded pdb=" OG SER C 12 " pdb=" OE1 GLU C 105 " model vdw 2.259 3.040 nonbonded pdb=" O ILE J 277 " pdb=" NH2 ARG J 456 " model vdw 2.309 3.120 nonbonded pdb=" NZ LYS L 24 " pdb=" OD2 ASP L 70 " model vdw 2.315 3.120 nonbonded pdb=" OG SER G 264 " pdb=" OE2 GLU G 482 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASN G 283 " pdb=" OG1 THR G 455 " model vdw 2.327 3.040 ... (remaining 147155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 512 through 662 or resid 701)) selection = (chain 'E' and (resid 512 through 662 or resid 701)) selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'T' selection = chain 'd' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 47.380 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.150 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 20631 Z= 0.268 Angle : 1.025 21.075 28196 Z= 0.509 Chirality : 0.058 0.474 3395 Planarity : 0.005 0.095 3416 Dihedral : 17.496 120.185 8915 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 0.09 % Allowed : 1.09 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.16), residues: 2343 helix: -3.31 (0.18), residues: 337 sheet: 0.51 (0.21), residues: 552 loop : -1.18 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 427 HIS 0.006 0.001 HIS I 89 PHE 0.020 0.001 PHE I 98 TYR 0.029 0.002 TYR F 50 ARG 0.065 0.002 ARG F 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 56) link_NAG-ASN : angle 3.59677 ( 168) link_ALPHA1-6 : bond 0.00903 ( 4) link_ALPHA1-6 : angle 1.85980 ( 12) link_BETA1-4 : bond 0.01073 ( 30) link_BETA1-4 : angle 3.32834 ( 90) link_ALPHA1-3 : bond 0.00996 ( 4) link_ALPHA1-3 : angle 1.78245 ( 12) hydrogen bonds : bond 0.28576 ( 564) hydrogen bonds : angle 9.96664 ( 1485) SS BOND : bond 0.00537 ( 42) SS BOND : angle 1.55605 ( 84) covalent geometry : bond 0.00533 (20495) covalent geometry : angle 0.96941 (27830) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 581 LEU cc_start: 0.7663 (tp) cc_final: 0.7323 (tp) REVERT: K 536 THR cc_start: 0.7416 (p) cc_final: 0.7184 (p) REVERT: K 624 ASP cc_start: 0.7083 (p0) cc_final: 0.6470 (p0) REVERT: L 20 SER cc_start: 0.7916 (p) cc_final: 0.7281 (t) REVERT: C 1 ASP cc_start: 0.7041 (m-30) cc_final: 0.6327 (t0) REVERT: C 3 VAL cc_start: 0.9264 (t) cc_final: 0.9007 (m) REVERT: F 35 TRP cc_start: 0.8002 (m100) cc_final: 0.7470 (m100) REVERT: F 48 MET cc_start: 0.7397 (ptp) cc_final: 0.7167 (mpp) REVERT: F 109 LEU cc_start: 0.6502 (mt) cc_final: 0.6215 (mm) REVERT: I 3 VAL cc_start: 0.8156 (t) cc_final: 0.7756 (p) REVERT: I 4 MET cc_start: 0.6818 (mmm) cc_final: 0.4651 (mtp) outliers start: 2 outliers final: 1 residues processed: 274 average time/residue: 0.3858 time to fit residues: 151.7736 Evaluate side-chains 123 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 183 optimal weight: 40.0000 chunk 70 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 212 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN B 543 ASN D 105 HIS D 398 ASN D 478 ASN E 653 GLN J 246 GLN ** J 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN K 550 GLN K 651 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN L 37 GLN ** L 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN I 6 GLN ** I 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.051959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.035954 restraints weight = 159486.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.037046 restraints weight = 85370.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.037738 restraints weight = 58502.439| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20631 Z= 0.216 Angle : 0.793 15.322 28196 Z= 0.384 Chirality : 0.048 0.378 3395 Planarity : 0.005 0.071 3416 Dihedral : 14.336 108.009 4497 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.65 % Favored : 95.22 % Rotamer: Outliers : 1.23 % Allowed : 8.00 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2343 helix: -0.96 (0.27), residues: 338 sheet: 0.51 (0.20), residues: 618 loop : -0.70 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 338 HIS 0.018 0.001 HIS C 8 PHE 0.019 0.002 PHE H 78 TYR 0.027 0.002 TYR H 33 ARG 0.008 0.001 ARG G 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 56) link_NAG-ASN : angle 2.95493 ( 168) link_ALPHA1-6 : bond 0.01311 ( 4) link_ALPHA1-6 : angle 2.34277 ( 12) link_BETA1-4 : bond 0.00696 ( 30) link_BETA1-4 : angle 2.51855 ( 90) link_ALPHA1-3 : bond 0.01488 ( 4) link_ALPHA1-3 : angle 2.79741 ( 12) hydrogen bonds : bond 0.04592 ( 564) hydrogen bonds : angle 6.42041 ( 1485) SS BOND : bond 0.00334 ( 42) SS BOND : angle 1.48375 ( 84) covalent geometry : bond 0.00466 (20495) covalent geometry : angle 0.74269 (27830) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 573 ILE cc_start: 0.9093 (pt) cc_final: 0.8853 (mp) REVERT: B 581 LEU cc_start: 0.9588 (tp) cc_final: 0.9387 (pp) REVERT: D 150 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7965 (mpp) REVERT: D 161 MET cc_start: 0.7844 (tmm) cc_final: 0.7391 (tmm) REVERT: E 530 MET cc_start: 0.8957 (mtp) cc_final: 0.8622 (mtp) REVERT: J 104 MET cc_start: 0.9064 (ppp) cc_final: 0.8855 (ppp) REVERT: J 390 LEU cc_start: 0.9627 (mt) cc_final: 0.9260 (tp) REVERT: K 581 LEU cc_start: 0.9677 (tt) cc_final: 0.9459 (pp) REVERT: K 589 ASP cc_start: 0.9400 (m-30) cc_final: 0.9059 (m-30) REVERT: K 624 ASP cc_start: 0.9194 (p0) cc_final: 0.8895 (p0) REVERT: L 54 ARG cc_start: 0.9411 (mtm-85) cc_final: 0.9198 (ptp-110) REVERT: L 70 ASP cc_start: 0.9025 (t0) cc_final: 0.8665 (p0) REVERT: A 65 ASN cc_start: 0.9386 (t0) cc_final: 0.9146 (p0) REVERT: I 4 MET cc_start: 0.6640 (mmm) cc_final: 0.4894 (mtp) outliers start: 26 outliers final: 17 residues processed: 150 average time/residue: 0.3226 time to fit residues: 74.3319 Evaluate side-chains 125 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 641 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 59 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 211 optimal weight: 40.0000 chunk 77 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 45 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 203 GLN ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN J 315 GLN ** J 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN A 5 GLN ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35AASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.051710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.035783 restraints weight = 161311.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.036637 restraints weight = 91597.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.037244 restraints weight = 65151.199| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20631 Z= 0.133 Angle : 0.685 14.508 28196 Z= 0.325 Chirality : 0.047 0.388 3395 Planarity : 0.004 0.059 3416 Dihedral : 11.968 105.675 4496 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.70 % Allowed : 9.42 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2343 helix: -0.20 (0.29), residues: 342 sheet: 0.43 (0.20), residues: 648 loop : -0.54 (0.18), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 47 HIS 0.012 0.001 HIS C 8 PHE 0.025 0.001 PHE H 78 TYR 0.023 0.001 TYR F 53 ARG 0.005 0.000 ARG C 9 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 56) link_NAG-ASN : angle 2.74825 ( 168) link_ALPHA1-6 : bond 0.01366 ( 4) link_ALPHA1-6 : angle 2.44910 ( 12) link_BETA1-4 : bond 0.00639 ( 30) link_BETA1-4 : angle 2.32945 ( 90) link_ALPHA1-3 : bond 0.01842 ( 4) link_ALPHA1-3 : angle 2.88914 ( 12) hydrogen bonds : bond 0.03734 ( 564) hydrogen bonds : angle 5.67393 ( 1485) SS BOND : bond 0.00270 ( 42) SS BOND : angle 1.26188 ( 84) covalent geometry : bond 0.00285 (20495) covalent geometry : angle 0.63399 (27830) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 198 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8335 (p) REVERT: B 530 MET cc_start: 0.9045 (mmt) cc_final: 0.7157 (mmm) REVERT: B 573 ILE cc_start: 0.9122 (pt) cc_final: 0.8881 (mp) REVERT: D 150 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8091 (mpp) REVERT: J 104 MET cc_start: 0.9104 (ppp) cc_final: 0.8691 (ppp) REVERT: J 390 LEU cc_start: 0.9593 (mt) cc_final: 0.9202 (tp) REVERT: K 581 LEU cc_start: 0.9694 (tt) cc_final: 0.9385 (mm) REVERT: K 589 ASP cc_start: 0.9427 (m-30) cc_final: 0.9209 (m-30) REVERT: K 624 ASP cc_start: 0.9149 (p0) cc_final: 0.8883 (p0) REVERT: L 70 ASP cc_start: 0.9016 (t0) cc_final: 0.8632 (p0) REVERT: A 65 ASN cc_start: 0.9458 (t0) cc_final: 0.9166 (p0) REVERT: I 4 MET cc_start: 0.6540 (mmm) cc_final: 0.4920 (mtp) REVERT: I 11 MET cc_start: 0.4756 (ptm) cc_final: 0.4096 (ptm) outliers start: 36 outliers final: 19 residues processed: 143 average time/residue: 0.3311 time to fit residues: 73.7978 Evaluate side-chains 118 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 641 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain F residue 40 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 127 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 224 optimal weight: 40.0000 chunk 205 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN J 377 ASN ** K 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN L 37 GLN A 5 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 39 GLN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.049952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.034110 restraints weight = 165625.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.035098 restraints weight = 90477.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.035713 restraints weight = 63081.591| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20631 Z= 0.252 Angle : 0.789 14.596 28196 Z= 0.373 Chirality : 0.047 0.357 3395 Planarity : 0.005 0.065 3416 Dihedral : 10.741 105.056 4496 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.13 % Allowed : 11.41 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2343 helix: 0.30 (0.29), residues: 358 sheet: 0.10 (0.20), residues: 672 loop : -0.37 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 45 HIS 0.008 0.001 HIS C 8 PHE 0.019 0.002 PHE B 522 TYR 0.017 0.002 TYR F 53 ARG 0.004 0.001 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 56) link_NAG-ASN : angle 3.01013 ( 168) link_ALPHA1-6 : bond 0.01589 ( 4) link_ALPHA1-6 : angle 2.58695 ( 12) link_BETA1-4 : bond 0.00571 ( 30) link_BETA1-4 : angle 2.32635 ( 90) link_ALPHA1-3 : bond 0.01960 ( 4) link_ALPHA1-3 : angle 3.26934 ( 12) hydrogen bonds : bond 0.03649 ( 564) hydrogen bonds : angle 5.45309 ( 1485) SS BOND : bond 0.00679 ( 42) SS BOND : angle 1.62238 ( 84) covalent geometry : bond 0.00547 (20495) covalent geometry : angle 0.73695 (27830) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 104 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 272 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9257 (mt) REVERT: G 390 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9072 (tp) REVERT: D 150 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8080 (mpp) REVERT: J 390 LEU cc_start: 0.9564 (mt) cc_final: 0.9209 (tp) REVERT: K 581 LEU cc_start: 0.9692 (tt) cc_final: 0.9386 (mm) REVERT: K 589 ASP cc_start: 0.9469 (m-30) cc_final: 0.9259 (m-30) REVERT: L 9 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7852 (mmp-170) REVERT: L 70 ASP cc_start: 0.9099 (t0) cc_final: 0.8796 (p0) REVERT: A 5 GLN cc_start: 0.9514 (tp-100) cc_final: 0.9024 (tm-30) REVERT: C 1 ASP cc_start: 0.7980 (m-30) cc_final: 0.7481 (t0) REVERT: C 13 THR cc_start: 0.6621 (OUTLIER) cc_final: 0.6101 (p) REVERT: C 18 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7493 (tmm-80) REVERT: I 4 MET cc_start: 0.6302 (mmm) cc_final: 0.4778 (mtp) outliers start: 45 outliers final: 26 residues processed: 141 average time/residue: 0.3104 time to fit residues: 69.6456 Evaluate side-chains 124 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 641 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 204 optimal weight: 0.9980 chunk 108 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.050508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.034855 restraints weight = 166202.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.035790 restraints weight = 89805.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.036419 restraints weight = 62608.482| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20631 Z= 0.132 Angle : 0.681 13.983 28196 Z= 0.321 Chirality : 0.046 0.398 3395 Planarity : 0.004 0.056 3416 Dihedral : 9.676 108.343 4496 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.70 % Allowed : 12.78 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2343 helix: 0.62 (0.30), residues: 357 sheet: 0.49 (0.21), residues: 627 loop : -0.49 (0.18), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 45 HIS 0.007 0.001 HIS C 8 PHE 0.023 0.001 PHE D 53 TYR 0.013 0.001 TYR F 53 ARG 0.004 0.000 ARG F 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 56) link_NAG-ASN : angle 2.78610 ( 168) link_ALPHA1-6 : bond 0.01702 ( 4) link_ALPHA1-6 : angle 2.61778 ( 12) link_BETA1-4 : bond 0.00568 ( 30) link_BETA1-4 : angle 2.19161 ( 90) link_ALPHA1-3 : bond 0.02099 ( 4) link_ALPHA1-3 : angle 3.26245 ( 12) hydrogen bonds : bond 0.03120 ( 564) hydrogen bonds : angle 5.15368 ( 1485) SS BOND : bond 0.00306 ( 42) SS BOND : angle 1.36089 ( 84) covalent geometry : bond 0.00288 (20495) covalent geometry : angle 0.62816 (27830) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8975 (mmt) cc_final: 0.7069 (mmm) REVERT: J 390 LEU cc_start: 0.9567 (mt) cc_final: 0.9152 (tp) REVERT: K 581 LEU cc_start: 0.9688 (tt) cc_final: 0.9349 (mm) REVERT: K 584 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8529 (mt-10) REVERT: K 589 ASP cc_start: 0.9460 (m-30) cc_final: 0.9229 (m-30) REVERT: L 4 MET cc_start: 0.4913 (ptp) cc_final: 0.4278 (pmm) REVERT: L 70 ASP cc_start: 0.9104 (t0) cc_final: 0.8796 (p0) REVERT: A 5 GLN cc_start: 0.9488 (tp-100) cc_final: 0.9108 (tm-30) REVERT: C 1 ASP cc_start: 0.8005 (m-30) cc_final: 0.7467 (t0) REVERT: C 13 THR cc_start: 0.6614 (OUTLIER) cc_final: 0.6100 (p) REVERT: F 29 ILE cc_start: 0.7432 (pt) cc_final: 0.6985 (mp) REVERT: I 4 MET cc_start: 0.6209 (mmm) cc_final: 0.4758 (mtp) outliers start: 36 outliers final: 22 residues processed: 130 average time/residue: 0.3090 time to fit residues: 63.4704 Evaluate side-chains 112 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 641 ILE Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 68 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 172 optimal weight: 50.0000 chunk 118 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 219 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN J 377 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.049448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.033790 restraints weight = 170661.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.034803 restraints weight = 93898.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.035428 restraints weight = 66190.523| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20631 Z= 0.240 Angle : 0.761 14.315 28196 Z= 0.359 Chirality : 0.047 0.364 3395 Planarity : 0.004 0.065 3416 Dihedral : 9.258 107.490 4496 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.23 % Allowed : 13.02 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2343 helix: 0.66 (0.30), residues: 359 sheet: 0.17 (0.20), residues: 666 loop : -0.44 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 45 HIS 0.011 0.001 HIS C 8 PHE 0.017 0.002 PHE B 522 TYR 0.015 0.001 TYR D 435 ARG 0.004 0.000 ARG G 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 56) link_NAG-ASN : angle 2.99036 ( 168) link_ALPHA1-6 : bond 0.01913 ( 4) link_ALPHA1-6 : angle 2.77780 ( 12) link_BETA1-4 : bond 0.00554 ( 30) link_BETA1-4 : angle 2.23357 ( 90) link_ALPHA1-3 : bond 0.02225 ( 4) link_ALPHA1-3 : angle 3.27106 ( 12) hydrogen bonds : bond 0.03376 ( 564) hydrogen bonds : angle 5.18263 ( 1485) SS BOND : bond 0.00462 ( 42) SS BOND : angle 1.66757 ( 84) covalent geometry : bond 0.00522 (20495) covalent geometry : angle 0.70705 (27830) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 90 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 272 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9154 (mt) REVERT: G 390 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9064 (tp) REVERT: E 642 ILE cc_start: 0.9698 (OUTLIER) cc_final: 0.9479 (pt) REVERT: J 271 MET cc_start: 0.8844 (mpp) cc_final: 0.8644 (mpp) REVERT: J 390 LEU cc_start: 0.9592 (mt) cc_final: 0.9302 (tp) REVERT: K 581 LEU cc_start: 0.9695 (tt) cc_final: 0.9313 (mm) REVERT: K 589 ASP cc_start: 0.9428 (m-30) cc_final: 0.9198 (m-30) REVERT: L 4 MET cc_start: 0.5072 (ptp) cc_final: 0.4466 (pmm) REVERT: L 70 ASP cc_start: 0.9184 (t0) cc_final: 0.8855 (p0) REVERT: A 5 GLN cc_start: 0.9492 (tp-100) cc_final: 0.9104 (tm-30) REVERT: C 1 ASP cc_start: 0.7989 (m-30) cc_final: 0.7633 (t0) REVERT: F 29 ILE cc_start: 0.7137 (pt) cc_final: 0.6700 (mp) REVERT: I 4 MET cc_start: 0.5968 (mmm) cc_final: 0.5066 (mtt) outliers start: 47 outliers final: 32 residues processed: 128 average time/residue: 0.3242 time to fit residues: 65.2963 Evaluate side-chains 118 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 641 ILE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 119 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 232 optimal weight: 20.0000 chunk 128 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 226 optimal weight: 20.0000 chunk 223 optimal weight: 0.0970 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.050227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.034693 restraints weight = 163635.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.035656 restraints weight = 87701.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.036278 restraints weight = 60885.062| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20631 Z= 0.119 Angle : 0.678 13.723 28196 Z= 0.317 Chirality : 0.045 0.406 3395 Planarity : 0.004 0.056 3416 Dihedral : 8.542 107.497 4496 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.70 % Allowed : 13.97 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2343 helix: 1.30 (0.31), residues: 327 sheet: 0.41 (0.20), residues: 639 loop : -0.47 (0.18), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 45 HIS 0.005 0.001 HIS C 8 PHE 0.014 0.001 PHE F 78 TYR 0.011 0.001 TYR A 90 ARG 0.009 0.000 ARG K 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 56) link_NAG-ASN : angle 2.75826 ( 168) link_ALPHA1-6 : bond 0.01834 ( 4) link_ALPHA1-6 : angle 2.84437 ( 12) link_BETA1-4 : bond 0.00581 ( 30) link_BETA1-4 : angle 2.14303 ( 90) link_ALPHA1-3 : bond 0.02492 ( 4) link_ALPHA1-3 : angle 3.38339 ( 12) hydrogen bonds : bond 0.02983 ( 564) hydrogen bonds : angle 4.93965 ( 1485) SS BOND : bond 0.00274 ( 42) SS BOND : angle 1.36315 ( 84) covalent geometry : bond 0.00257 (20495) covalent geometry : angle 0.62482 (27830) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8990 (mmt) cc_final: 0.8060 (tpp) REVERT: E 642 ILE cc_start: 0.9699 (OUTLIER) cc_final: 0.9479 (pt) REVERT: J 100 MET cc_start: 0.9192 (mtp) cc_final: 0.8922 (mtm) REVERT: J 104 MET cc_start: 0.9179 (ppp) cc_final: 0.8914 (ppp) REVERT: J 271 MET cc_start: 0.8793 (mpp) cc_final: 0.8518 (mpp) REVERT: J 390 LEU cc_start: 0.9573 (mt) cc_final: 0.9186 (tp) REVERT: K 581 LEU cc_start: 0.9691 (tt) cc_final: 0.9408 (mm) REVERT: K 589 ASP cc_start: 0.9412 (m-30) cc_final: 0.9163 (m-30) REVERT: K 657 GLU cc_start: 0.9592 (tm-30) cc_final: 0.9387 (pp20) REVERT: L 4 MET cc_start: 0.5348 (ptp) cc_final: 0.4724 (pmm) REVERT: L 70 ASP cc_start: 0.9178 (t0) cc_final: 0.8863 (p0) REVERT: C 1 ASP cc_start: 0.7986 (m-30) cc_final: 0.7619 (t0) REVERT: F 29 ILE cc_start: 0.7561 (pt) cc_final: 0.7015 (mp) REVERT: I 4 MET cc_start: 0.6074 (mmm) cc_final: 0.5032 (mtt) outliers start: 36 outliers final: 28 residues processed: 124 average time/residue: 0.3216 time to fit residues: 61.8670 Evaluate side-chains 118 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 530 MET Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 641 ILE Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 161 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 109 optimal weight: 0.0870 chunk 158 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.050182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.034621 restraints weight = 165831.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.035614 restraints weight = 89113.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.036208 restraints weight = 61878.420| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20631 Z= 0.119 Angle : 0.663 13.671 28196 Z= 0.310 Chirality : 0.045 0.393 3395 Planarity : 0.004 0.055 3416 Dihedral : 7.972 104.259 4496 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.75 % Allowed : 13.97 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2343 helix: 1.42 (0.31), residues: 327 sheet: 0.46 (0.21), residues: 603 loop : -0.46 (0.18), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 45 HIS 0.004 0.001 HIS C 8 PHE 0.013 0.001 PHE H 78 TYR 0.012 0.001 TYR A 90 ARG 0.006 0.000 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 56) link_NAG-ASN : angle 2.71144 ( 168) link_ALPHA1-6 : bond 0.01839 ( 4) link_ALPHA1-6 : angle 2.97047 ( 12) link_BETA1-4 : bond 0.00577 ( 30) link_BETA1-4 : angle 2.12685 ( 90) link_ALPHA1-3 : bond 0.02649 ( 4) link_ALPHA1-3 : angle 3.56527 ( 12) hydrogen bonds : bond 0.02874 ( 564) hydrogen bonds : angle 4.75237 ( 1485) SS BOND : bond 0.00278 ( 42) SS BOND : angle 1.27323 ( 84) covalent geometry : bond 0.00259 (20495) covalent geometry : angle 0.60965 (27830) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8990 (mmt) cc_final: 0.8023 (tpp) REVERT: J 100 MET cc_start: 0.9150 (mtp) cc_final: 0.8873 (mtm) REVERT: J 104 MET cc_start: 0.9156 (ppp) cc_final: 0.8868 (ppp) REVERT: J 271 MET cc_start: 0.8812 (mpp) cc_final: 0.8507 (mpp) REVERT: J 390 LEU cc_start: 0.9581 (mt) cc_final: 0.9185 (tp) REVERT: K 581 LEU cc_start: 0.9680 (tt) cc_final: 0.9352 (mm) REVERT: K 589 ASP cc_start: 0.9420 (m-30) cc_final: 0.9169 (m-30) REVERT: H 64 LYS cc_start: 0.9516 (pptt) cc_final: 0.9278 (pptt) REVERT: H 65 ASN cc_start: 0.8601 (m-40) cc_final: 0.8322 (t0) REVERT: L 4 MET cc_start: 0.5412 (ptp) cc_final: 0.4787 (pmm) REVERT: L 70 ASP cc_start: 0.9203 (t0) cc_final: 0.8895 (p0) REVERT: C 1 ASP cc_start: 0.8021 (m-30) cc_final: 0.7652 (t0) REVERT: F 29 ILE cc_start: 0.7536 (pt) cc_final: 0.7020 (mp) REVERT: I 4 MET cc_start: 0.6080 (mmm) cc_final: 0.5046 (mtt) outliers start: 37 outliers final: 28 residues processed: 122 average time/residue: 0.3104 time to fit residues: 60.5759 Evaluate side-chains 117 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 641 ILE Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 51 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 209 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 HIS D 258 GLN D 328 GLN E 616 ASN ** J 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 398 ASN ** K 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.047804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.032202 restraints weight = 165167.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.033149 restraints weight = 91273.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.033753 restraints weight = 64466.200| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 20631 Z= 0.334 Angle : 0.895 14.395 28196 Z= 0.422 Chirality : 0.048 0.336 3395 Planarity : 0.006 0.128 3416 Dihedral : 8.761 96.993 4496 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.08 % Allowed : 14.20 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2343 helix: 0.55 (0.29), residues: 359 sheet: -0.11 (0.19), residues: 690 loop : -0.54 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 614 HIS 0.011 0.002 HIS G 216 PHE 0.027 0.002 PHE B 522 TYR 0.018 0.002 TYR D 435 ARG 0.006 0.001 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00793 ( 56) link_NAG-ASN : angle 3.23392 ( 168) link_ALPHA1-6 : bond 0.01811 ( 4) link_ALPHA1-6 : angle 2.94625 ( 12) link_BETA1-4 : bond 0.00634 ( 30) link_BETA1-4 : angle 2.32806 ( 90) link_ALPHA1-3 : bond 0.02521 ( 4) link_ALPHA1-3 : angle 3.27430 ( 12) hydrogen bonds : bond 0.03820 ( 564) hydrogen bonds : angle 5.26762 ( 1485) SS BOND : bond 0.00618 ( 42) SS BOND : angle 2.06903 ( 84) covalent geometry : bond 0.00726 (20495) covalent geometry : angle 0.84205 (27830) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 89 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 161 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7518 (tmm) REVERT: E 616 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8376 (m110) REVERT: J 271 MET cc_start: 0.8841 (mpp) cc_final: 0.8593 (mpp) REVERT: K 581 LEU cc_start: 0.9686 (tt) cc_final: 0.9344 (mm) REVERT: K 589 ASP cc_start: 0.9455 (m-30) cc_final: 0.9227 (m-30) REVERT: L 4 MET cc_start: 0.5555 (ptp) cc_final: 0.5244 (ptp) REVERT: L 9 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7767 (mmp-170) REVERT: L 70 ASP cc_start: 0.9268 (t0) cc_final: 0.8983 (p0) REVERT: C 1 ASP cc_start: 0.8223 (m-30) cc_final: 0.7886 (t0) REVERT: F 29 ILE cc_start: 0.7029 (pt) cc_final: 0.6562 (mp) REVERT: I 4 MET cc_start: 0.5608 (mmm) cc_final: 0.4804 (mtt) outliers start: 44 outliers final: 31 residues processed: 121 average time/residue: 0.3127 time to fit residues: 60.5118 Evaluate side-chains 113 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 530 MET Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 610 TRP Chi-restraints excluded: chain K residue 641 ILE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 153 optimal weight: 0.0670 chunk 95 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 217 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 180 optimal weight: 40.0000 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 GLN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.048786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.033298 restraints weight = 171052.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.034323 restraints weight = 93200.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.034965 restraints weight = 65379.458| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20631 Z= 0.194 Angle : 0.748 13.863 28196 Z= 0.355 Chirality : 0.046 0.382 3395 Planarity : 0.004 0.087 3416 Dihedral : 8.485 98.232 4496 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.70 % Allowed : 14.54 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2343 helix: 0.99 (0.30), residues: 350 sheet: -0.13 (0.20), residues: 648 loop : -0.51 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 614 HIS 0.010 0.001 HIS C 8 PHE 0.013 0.002 PHE B 522 TYR 0.015 0.001 TYR A 90 ARG 0.011 0.001 ARG F 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 56) link_NAG-ASN : angle 2.99332 ( 168) link_ALPHA1-6 : bond 0.01808 ( 4) link_ALPHA1-6 : angle 2.92985 ( 12) link_BETA1-4 : bond 0.00543 ( 30) link_BETA1-4 : angle 2.18109 ( 90) link_ALPHA1-3 : bond 0.02546 ( 4) link_ALPHA1-3 : angle 3.48147 ( 12) hydrogen bonds : bond 0.03241 ( 564) hydrogen bonds : angle 5.05069 ( 1485) SS BOND : bond 0.00424 ( 42) SS BOND : angle 1.65557 ( 84) covalent geometry : bond 0.00424 (20495) covalent geometry : angle 0.69343 (27830) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 161 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7633 (tmm) REVERT: J 271 MET cc_start: 0.8832 (mpp) cc_final: 0.8567 (mpp) REVERT: K 589 ASP cc_start: 0.9420 (m-30) cc_final: 0.9186 (m-30) REVERT: L 4 MET cc_start: 0.5694 (ptp) cc_final: 0.5436 (ptp) REVERT: L 9 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7809 (mmp-170) REVERT: L 70 ASP cc_start: 0.9281 (t0) cc_final: 0.9006 (p0) REVERT: A 5 GLN cc_start: 0.9446 (OUTLIER) cc_final: 0.9086 (tm-30) REVERT: F 29 ILE cc_start: 0.6870 (pt) cc_final: 0.6401 (mp) REVERT: I 4 MET cc_start: 0.4986 (mmm) cc_final: 0.4259 (mtt) outliers start: 36 outliers final: 32 residues processed: 108 average time/residue: 0.3232 time to fit residues: 55.7034 Evaluate side-chains 113 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 530 MET Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 610 TRP Chi-restraints excluded: chain K residue 641 ILE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 107 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.048692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.033181 restraints weight = 167892.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.034192 restraints weight = 89362.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.034844 restraints weight = 62004.931| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 20631 Z= 0.215 Angle : 0.883 58.944 28196 Z= 0.460 Chirality : 0.046 0.388 3395 Planarity : 0.004 0.087 3416 Dihedral : 8.488 98.305 4496 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.89 % Allowed : 14.63 % Favored : 83.48 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2343 helix: 0.99 (0.30), residues: 350 sheet: -0.15 (0.20), residues: 648 loop : -0.52 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 614 HIS 0.008 0.001 HIS C 8 PHE 0.013 0.001 PHE F 78 TYR 0.011 0.001 TYR A 90 ARG 0.011 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 56) link_NAG-ASN : angle 2.98539 ( 168) link_ALPHA1-6 : bond 0.01816 ( 4) link_ALPHA1-6 : angle 2.97880 ( 12) link_BETA1-4 : bond 0.00535 ( 30) link_BETA1-4 : angle 2.17520 ( 90) link_ALPHA1-3 : bond 0.02541 ( 4) link_ALPHA1-3 : angle 3.50179 ( 12) hydrogen bonds : bond 0.03347 ( 564) hydrogen bonds : angle 5.06361 ( 1485) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.62801 ( 84) covalent geometry : bond 0.00477 (20495) covalent geometry : angle 0.83922 (27830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6191.88 seconds wall clock time: 109 minutes 47.26 seconds (6587.26 seconds total)