Starting phenix.real_space_refine on Wed Jun 18 15:35:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t74_25733/06_2025/7t74_25733.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t74_25733/06_2025/7t74_25733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t74_25733/06_2025/7t74_25733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t74_25733/06_2025/7t74_25733.map" model { file = "/net/cci-nas-00/data/ceres_data/7t74_25733/06_2025/7t74_25733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t74_25733/06_2025/7t74_25733.cif" } resolution = 3.35 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= 0.000 sd= 0.033 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 13254 2.51 5 N 3523 2.21 5 O 4293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21199 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "H" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1018 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "F" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 962 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "I" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "J" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 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: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 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: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: 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: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "i" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 13.73, per 1000 atoms: 0.65 Number of scatterers: 21199 At special positions: 0 Unit cell: (128.75, 121.54, 190.55, 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 4293 8.00 N 3523 7.00 C 13254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.06 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 7 " " MAN O 4 " - " MAN O 5 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 6 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG T 1 " - " FUC T 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 2 " " NAG a 1 " - " FUC a 2 " " NAG b 1 " - " FUC b 2 " " NAG h 1 " - " FUC h 2 " " NAG i 1 " - " FUC i 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 355 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 197 " " NAG A 612 " - " ASN A 133 " " NAG B 701 " - " ASN B 625 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 355 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG D 701 " - " ASN D 625 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 133 " " NAG F 701 " - " ASN F 625 " " NAG F 702 " - " ASN F 637 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 332 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN B 618 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN D 618 " " NAG b 1 " - " ASN D 611 " " NAG c 1 " - " ASN E 160 " " NAG d 1 " - " ASN E 386 " " NAG e 1 " - " ASN E 332 " " NAG f 1 " - " ASN E 262 " " NAG g 1 " - " ASN E 156 " " NAG h 1 " - " ASN F 618 " " NAG i 1 " - " ASN F 611 " Time building additional restraints: 6.04 Conformation dependent library (CDL) restraints added in 2.7 seconds 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 37 sheets defined 20.7% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.695A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.684A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 194 through 199 removed outlier: 4.503A pdb=" N THR A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.951A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.426A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.722A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.559A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.531A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 526 removed outlier: 4.326A pdb=" N GLY D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 532 Processing helix chain 'D' and resid 534 through 540 Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.673A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.265A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.520A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 532 Processing helix chain 'F' and resid 534 through 540 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.512A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.776A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.570A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.830A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'K' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 11 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'G' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 12 through 13 current: chain 'G' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 48 current: chain 'G' and resid 96 through 98 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.554A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.552A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.822A pdb=" N PHE L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR L 50 " --> pdb=" O PHE L 34 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.954A pdb=" N MET H 34 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N HIS H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100H through 103 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.413A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.672A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.539A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 7.005A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AC5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=AC7, first strand: chain 'N' and resid 11 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 11 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.392A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.795A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD4, first strand: chain 'E' and resid 169 through 177 removed outlier: 5.190A pdb=" N THR E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) removed outlier: 11.389A pdb=" N ASN E 133 " --> pdb=" O ASN E 187 " (cutoff:3.500A) removed outlier: 16.671A pdb=" N ASN E 187 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASN E 190 " --> pdb=" O MET E 184 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.593A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.773A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 11 through 12 current: chain 'I' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100H through 103 Processing sheet with id=AD9, first strand: chain 'J' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 12 through 13 current: chain 'J' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 45 through 48 current: chain 'J' and resid 96 through 98 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 19 through 24 590 hydrogen bonds defined for protein. 1521 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: 6.55 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4488 1.32 - 1.46: 7000 1.46 - 1.59: 9893 1.59 - 1.73: 60 1.73 - 1.87: 175 Bond restraints: 21616 Sorted by residual: bond pdb=" CB HIS B 570 " pdb=" CG HIS B 570 " ideal model delta sigma weight residual 1.497 1.582 -0.085 1.40e-02 5.10e+03 3.71e+01 bond pdb=" CB ASP J 27B" pdb=" CG ASP J 27B" ideal model delta sigma weight residual 1.516 1.364 0.152 2.50e-02 1.60e+03 3.70e+01 bond pdb=" CB LEU N 107 " pdb=" CG LEU N 107 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CB ASP N 27B" pdb=" CG ASP N 27B" ideal model delta sigma weight residual 1.516 1.369 0.147 2.50e-02 1.60e+03 3.44e+01 bond pdb=" CB LEU J 107 " pdb=" CG LEU J 107 " ideal model delta sigma weight residual 1.530 1.645 -0.115 2.00e-02 2.50e+03 3.30e+01 ... (remaining 21611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.67: 29284 7.67 - 15.33: 34 15.33 - 23.00: 0 23.00 - 30.66: 0 30.66 - 38.33: 5 Bond angle restraints: 29323 Sorted by residual: angle pdb=" C2 NAG e 1 " pdb=" N2 NAG e 1 " pdb=" C7 NAG e 1 " ideal model delta sigma weight residual 124.56 162.89 -38.33 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C2 NAG b 1 " pdb=" N2 NAG b 1 " pdb=" C7 NAG b 1 " ideal model delta sigma weight residual 124.56 162.59 -38.03 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C2 NAG Q 1 " pdb=" N2 NAG Q 1 " pdb=" C7 NAG Q 1 " ideal model delta sigma weight residual 124.56 161.34 -36.78 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C2 NAG B 701 " pdb=" N2 NAG B 701 " pdb=" C7 NAG B 701 " ideal model delta sigma weight residual 124.56 160.92 -36.36 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG D 701 " pdb=" N2 NAG D 701 " pdb=" C7 NAG D 701 " ideal model delta sigma weight residual 124.56 160.82 -36.26 3.00e+00 1.11e-01 1.46e+02 ... (remaining 29318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.89: 13660 23.89 - 47.79: 296 47.79 - 71.68: 84 71.68 - 95.57: 43 95.57 - 119.47: 28 Dihedral angle restraints: 14111 sinusoidal: 6824 harmonic: 7287 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -125.73 39.73 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -123.97 37.97 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -123.91 37.91 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 14108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.038: 3548 1.038 - 2.076: 0 2.076 - 3.114: 0 3.114 - 4.151: 0 4.151 - 5.189: 1 Chirality restraints: 3549 Sorted by residual: chirality pdb=" C4 FUC i 2 " pdb=" C3 FUC i 2 " pdb=" C5 FUC i 2 " pdb=" O4 FUC i 2 " both_signs ideal model delta sigma weight residual False -2.49 2.70 -5.19 2.00e-01 2.50e+01 6.73e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.94e+02 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 ... (remaining 3546 not shown) Planarity restraints: 3673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 702 " 0.256 2.00e-02 2.50e+03 2.19e-01 5.97e+02 pdb=" C7 NAG F 702 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG F 702 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG F 702 " -0.363 2.00e-02 2.50e+03 pdb=" O7 NAG F 702 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " -0.240 2.00e-02 2.50e+03 2.02e-01 5.11e+02 pdb=" C7 NAG c 2 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " 0.342 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 1 " -0.179 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" C7 NAG c 1 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG c 1 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG c 1 " 0.242 2.00e-02 2.50e+03 pdb=" O7 NAG c 1 " 0.020 2.00e-02 2.50e+03 ... (remaining 3670 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6602 2.85 - 3.36: 18676 3.36 - 3.87: 35487 3.87 - 4.39: 42075 4.39 - 4.90: 67263 Nonbonded interactions: 170103 Sorted by model distance: nonbonded pdb=" C THR H 100L" pdb=" OG1 THR H 100L" model vdw 2.337 2.616 nonbonded pdb=" N ASP K 84 " pdb=" OD1 ASP K 84 " model vdw 2.362 3.120 nonbonded pdb=" N ASP I 84 " pdb=" OD1 ASP I 84 " model vdw 2.363 3.120 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.364 3.120 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.390 3.120 ... (remaining 170098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'F' and (resid 518 through 661 or (resid 662 and (name N or name CA or na \ me C or name O or name CB )) or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'Y' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 49.730 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.023 0.152 21751 Z= 1.205 Angle : 1.798 38.326 29691 Z= 1.126 Chirality : 0.160 5.189 3549 Planarity : 0.010 0.219 3610 Dihedral : 12.706 119.466 9338 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.56 % Allowed : 2.48 % Favored : 96.96 % Rotamer: Outliers : 0.64 % Allowed : 0.91 % Favored : 98.45 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % 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: 0.71 (0.16), residues: 2497 helix: 0.10 (0.24), residues: 390 sheet: 0.81 (0.18), residues: 817 loop : 0.53 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.009 TRP C 96 HIS 0.012 0.003 HIS H 50 PHE 0.034 0.006 PHE E 353 TYR 0.049 0.007 TYR J 96 ARG 0.010 0.001 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.07559 ( 63) link_NAG-ASN : angle 2.83916 ( 189) link_ALPHA1-6 : bond 0.00814 ( 2) link_ALPHA1-6 : angle 1.64499 ( 6) link_BETA1-4 : bond 0.06176 ( 21) link_BETA1-4 : angle 4.53813 ( 63) link_ALPHA1-3 : bond 0.06562 ( 6) link_ALPHA1-3 : angle 4.16153 ( 18) hydrogen bonds : bond 0.16605 ( 590) hydrogen bonds : angle 6.64191 ( 1521) link_BETA1-6 : bond 0.07806 ( 6) link_BETA1-6 : angle 4.25299 ( 18) SS BOND : bond 0.00884 ( 37) SS BOND : angle 2.55441 ( 74) covalent geometry : bond 0.02239 (21616) covalent geometry : angle 1.77186 (29323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 408 time to evaluate : 2.359 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: G 5 THR cc_start: 0.8628 (m) cc_final: 0.8338 (p) REVERT: G 24 THR cc_start: 0.8937 (m) cc_final: 0.8523 (p) REVERT: L 34 PHE cc_start: 0.7476 (t80) cc_final: 0.7149 (t80) REVERT: L 40 ARG cc_start: 0.8939 (tmt170) cc_final: 0.8712 (tpp-160) REVERT: L 47 LEU cc_start: 0.5709 (tp) cc_final: 0.5147 (tp) REVERT: L 96 PHE cc_start: 0.4907 (m-80) cc_final: 0.4670 (m-80) REVERT: H 34 MET cc_start: 0.5555 (mmm) cc_final: 0.4653 (mmm) REVERT: H 78 LEU cc_start: 0.7303 (tp) cc_final: 0.6928 (tp) REVERT: H 93 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5426 (ppp) REVERT: C 207 LYS cc_start: 0.8564 (pttt) cc_final: 0.8315 (tmtt) REVERT: M 28 THR cc_start: 0.9154 (m) cc_final: 0.8829 (p) REVERT: M 68 THR cc_start: 0.9255 (m) cc_final: 0.9051 (p) REVERT: N 94 ARG cc_start: 0.5968 (mpt180) cc_final: 0.4893 (mmt180) REVERT: E 187 ASN cc_start: 0.6751 (t0) cc_final: 0.6474 (m-40) REVERT: F 632 ASP cc_start: 0.8550 (t70) cc_final: 0.8304 (t0) REVERT: J 94 ARG cc_start: 0.5959 (mpt180) cc_final: 0.4971 (mtp85) REVERT: J 97 ILE cc_start: 0.9134 (pt) cc_final: 0.8920 (pt) outliers start: 14 outliers final: 4 residues processed: 417 average time/residue: 0.4029 time to fit residues: 243.7285 Evaluate side-chains 226 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 221 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 201 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 570 HIS G 6 GLN C 187 ASN N 6 GLN N 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.092574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068887 restraints weight = 50563.407| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.32 r_work: 0.2931 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21751 Z= 0.171 Angle : 0.738 17.527 29691 Z= 0.365 Chirality : 0.049 0.793 3549 Planarity : 0.004 0.044 3610 Dihedral : 9.449 81.606 4761 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.00 % Rotamer: Outliers : 1.86 % Allowed : 5.59 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % 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: 0.72 (0.16), residues: 2497 helix: 1.97 (0.27), residues: 378 sheet: 0.71 (0.18), residues: 838 loop : -0.06 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 479 HIS 0.008 0.001 HIS B 570 PHE 0.022 0.002 PHE L 84 TYR 0.018 0.001 TYR C 173 ARG 0.008 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 63) link_NAG-ASN : angle 2.88343 ( 189) link_ALPHA1-6 : bond 0.00394 ( 2) link_ALPHA1-6 : angle 1.66719 ( 6) link_BETA1-4 : bond 0.00791 ( 21) link_BETA1-4 : angle 2.92200 ( 63) link_ALPHA1-3 : bond 0.01151 ( 6) link_ALPHA1-3 : angle 2.55234 ( 18) hydrogen bonds : bond 0.05459 ( 590) hydrogen bonds : angle 5.01545 ( 1521) link_BETA1-6 : bond 0.00936 ( 6) link_BETA1-6 : angle 1.24281 ( 18) SS BOND : bond 0.00307 ( 37) SS BOND : angle 0.98987 ( 74) covalent geometry : bond 0.00375 (21616) covalent geometry : angle 0.68662 (29323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7888 (mtm180) REVERT: K 34 MET cc_start: 0.8760 (mtt) cc_final: 0.8554 (mtm) REVERT: K 72 ASP cc_start: 0.8021 (t0) cc_final: 0.7544 (t70) REVERT: G 5 THR cc_start: 0.8711 (m) cc_final: 0.8328 (p) REVERT: G 24 THR cc_start: 0.9217 (m) cc_final: 0.8625 (p) REVERT: L 33 TYR cc_start: 0.7686 (m-80) cc_final: 0.7390 (m-80) REVERT: L 34 PHE cc_start: 0.7287 (t80) cc_final: 0.6945 (t80) REVERT: L 36 TRP cc_start: 0.7646 (m100) cc_final: 0.7430 (m100) REVERT: L 54 ARG cc_start: 0.7713 (mtp85) cc_final: 0.7479 (mtp85) REVERT: L 63 PHE cc_start: 0.7859 (m-80) cc_final: 0.7179 (m-80) REVERT: H 46 GLU cc_start: 0.8101 (tt0) cc_final: 0.7559 (tt0) REVERT: H 66 ARG cc_start: 0.7520 (ptp-170) cc_final: 0.6989 (ptm160) REVERT: H 79 TYR cc_start: 0.7551 (m-10) cc_final: 0.7326 (m-10) REVERT: H 93 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.6927 (ppp) REVERT: C 207 LYS cc_start: 0.8791 (pttt) cc_final: 0.8337 (tmtt) REVERT: C 475 MET cc_start: 0.8935 (mmm) cc_final: 0.8695 (tpp) REVERT: D 588 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8231 (mtt-85) REVERT: M 28 THR cc_start: 0.8749 (m) cc_final: 0.8325 (p) REVERT: M 43 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8252 (mmmt) REVERT: M 110 THR cc_start: 0.8903 (m) cc_final: 0.8667 (t) REVERT: N 60 ASP cc_start: 0.8223 (p0) cc_final: 0.6863 (t0) REVERT: N 83 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7528 (mm-30) REVERT: N 91 TYR cc_start: 0.9141 (t80) cc_final: 0.8892 (t80) REVERT: N 94 ARG cc_start: 0.5659 (mpt180) cc_final: 0.4301 (mmt180) REVERT: F 571 TRP cc_start: 0.7228 (t-100) cc_final: 0.7024 (t60) REVERT: J 31 ASN cc_start: 0.8669 (m-40) cc_final: 0.8337 (m110) REVERT: J 94 ARG cc_start: 0.5684 (mpt180) cc_final: 0.4599 (mtp85) outliers start: 41 outliers final: 16 residues processed: 308 average time/residue: 0.3858 time to fit residues: 174.3504 Evaluate side-chains 236 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 97 optimal weight: 9.9990 chunk 201 optimal weight: 0.0070 chunk 75 optimal weight: 20.0000 chunk 197 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.091465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.067217 restraints weight = 51320.222| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.46 r_work: 0.2901 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21751 Z= 0.145 Angle : 0.656 23.342 29691 Z= 0.318 Chirality : 0.047 0.627 3549 Planarity : 0.004 0.063 3610 Dihedral : 7.770 72.402 4756 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 2.05 % Allowed : 6.86 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % 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: 0.68 (0.17), residues: 2497 helix: 2.18 (0.28), residues: 384 sheet: 0.81 (0.18), residues: 816 loop : -0.28 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 47 HIS 0.005 0.001 HIS C 105 PHE 0.028 0.002 PHE L 96 TYR 0.014 0.001 TYR C 173 ARG 0.009 0.000 ARG M 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00740 ( 63) link_NAG-ASN : angle 2.85198 ( 189) link_ALPHA1-6 : bond 0.00233 ( 2) link_ALPHA1-6 : angle 1.69392 ( 6) link_BETA1-4 : bond 0.00582 ( 21) link_BETA1-4 : angle 2.19695 ( 63) link_ALPHA1-3 : bond 0.01047 ( 6) link_ALPHA1-3 : angle 2.18962 ( 18) hydrogen bonds : bond 0.04317 ( 590) hydrogen bonds : angle 4.53065 ( 1521) link_BETA1-6 : bond 0.00425 ( 6) link_BETA1-6 : angle 1.27761 ( 18) SS BOND : bond 0.00335 ( 37) SS BOND : angle 0.86496 ( 74) covalent geometry : bond 0.00327 (21616) covalent geometry : angle 0.60553 (29323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8052 (p90) cc_final: 0.7763 (p90) REVERT: A 143 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7559 (mtt-85) REVERT: A 184 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7616 (ttp) REVERT: K 4 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8063 (mm) REVERT: K 72 ASP cc_start: 0.8053 (t0) cc_final: 0.7469 (t70) REVERT: G 5 THR cc_start: 0.8760 (m) cc_final: 0.8379 (p) REVERT: G 103 ARG cc_start: 0.8478 (tpp-160) cc_final: 0.8087 (mtp85) REVERT: L 13 LEU cc_start: 0.7252 (mt) cc_final: 0.7006 (mp) REVERT: L 33 TYR cc_start: 0.7726 (m-80) cc_final: 0.7454 (m-80) REVERT: L 54 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7462 (mtp85) REVERT: L 63 PHE cc_start: 0.7302 (m-80) cc_final: 0.6971 (m-80) REVERT: H 71 ARG cc_start: 0.6507 (ttm110) cc_final: 0.5969 (ttm170) REVERT: H 72 ASP cc_start: 0.7551 (p0) cc_final: 0.7162 (p0) REVERT: H 100 ASP cc_start: 0.8649 (t0) cc_final: 0.8449 (t0) REVERT: C 207 LYS cc_start: 0.8734 (pttt) cc_final: 0.8283 (tmtt) REVERT: C 475 MET cc_start: 0.8925 (mmm) cc_final: 0.8681 (tpt) REVERT: D 624 ASP cc_start: 0.9027 (m-30) cc_final: 0.8295 (m-30) REVERT: D 654 GLU cc_start: 0.8317 (tt0) cc_final: 0.7945 (mt-10) REVERT: M 19 LYS cc_start: 0.8643 (tttt) cc_final: 0.8219 (tttp) REVERT: M 28 THR cc_start: 0.8698 (m) cc_final: 0.8321 (p) REVERT: M 43 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8164 (mmmt) REVERT: M 72 ASP cc_start: 0.7701 (t0) cc_final: 0.7488 (t0) REVERT: M 110 THR cc_start: 0.8960 (m) cc_final: 0.8714 (t) REVERT: N 60 ASP cc_start: 0.8194 (p0) cc_final: 0.6965 (t0) REVERT: N 83 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7476 (mm-30) REVERT: N 91 TYR cc_start: 0.9200 (t80) cc_final: 0.8946 (t80) REVERT: N 94 ARG cc_start: 0.5580 (mpt180) cc_final: 0.4222 (mmt180) REVERT: I 82 MET cc_start: 0.7984 (mtm) cc_final: 0.7735 (mtm) REVERT: J 17 GLN cc_start: 0.7617 (mp10) cc_final: 0.7346 (pt0) REVERT: J 27 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: J 31 ASN cc_start: 0.8808 (m-40) cc_final: 0.8508 (m-40) REVERT: J 79 GLN cc_start: 0.6898 (mp10) cc_final: 0.6634 (mp10) REVERT: J 94 ARG cc_start: 0.5876 (mpt180) cc_final: 0.4612 (mtp85) outliers start: 45 outliers final: 23 residues processed: 275 average time/residue: 0.4296 time to fit residues: 175.7951 Evaluate side-chains 241 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 161 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 236 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.088362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.064156 restraints weight = 52548.529| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.40 r_work: 0.2838 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21751 Z= 0.231 Angle : 0.693 22.259 29691 Z= 0.338 Chirality : 0.049 0.758 3549 Planarity : 0.004 0.037 3610 Dihedral : 6.794 64.765 4753 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 2.27 % Allowed : 7.18 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % 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: 0.40 (0.17), residues: 2497 helix: 1.94 (0.28), residues: 384 sheet: 0.73 (0.19), residues: 773 loop : -0.50 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 36 HIS 0.006 0.001 HIS C 105 PHE 0.027 0.002 PHE C 53 TYR 0.018 0.002 TYR M 27 ARG 0.005 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 63) link_NAG-ASN : angle 2.73937 ( 189) link_ALPHA1-6 : bond 0.00270 ( 2) link_ALPHA1-6 : angle 1.82335 ( 6) link_BETA1-4 : bond 0.00483 ( 21) link_BETA1-4 : angle 2.22360 ( 63) link_ALPHA1-3 : bond 0.00923 ( 6) link_ALPHA1-3 : angle 2.49913 ( 18) hydrogen bonds : bond 0.04780 ( 590) hydrogen bonds : angle 4.55920 ( 1521) link_BETA1-6 : bond 0.00333 ( 6) link_BETA1-6 : angle 1.38733 ( 18) SS BOND : bond 0.00386 ( 37) SS BOND : angle 0.90587 ( 74) covalent geometry : bond 0.00541 (21616) covalent geometry : angle 0.64792 (29323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7831 (ttp) REVERT: K 72 ASP cc_start: 0.8255 (t0) cc_final: 0.7666 (t70) REVERT: G 66 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8542 (ptmt) REVERT: G 103 ARG cc_start: 0.8324 (tpp-160) cc_final: 0.7973 (mtp85) REVERT: L 13 LEU cc_start: 0.7290 (mt) cc_final: 0.7010 (mp) REVERT: L 33 TYR cc_start: 0.7961 (m-80) cc_final: 0.7564 (m-10) REVERT: L 49 ILE cc_start: 0.8689 (mp) cc_final: 0.8120 (tt) REVERT: L 54 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7327 (mtp85) REVERT: L 90 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.8046 (ttm-80) REVERT: H 46 GLU cc_start: 0.8286 (tt0) cc_final: 0.8027 (tt0) REVERT: H 47 TRP cc_start: 0.7358 (t60) cc_final: 0.7038 (t60) REVERT: H 66 ARG cc_start: 0.7774 (mtm110) cc_final: 0.7505 (ptp-170) REVERT: H 72 ASP cc_start: 0.7765 (p0) cc_final: 0.7380 (p0) REVERT: H 79 TYR cc_start: 0.7527 (m-10) cc_final: 0.7180 (m-80) REVERT: C 207 LYS cc_start: 0.8612 (pttt) cc_final: 0.8210 (tmtt) REVERT: D 624 ASP cc_start: 0.8985 (m-30) cc_final: 0.8313 (m-30) REVERT: D 654 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: M 19 LYS cc_start: 0.8940 (tttt) cc_final: 0.8706 (tttp) REVERT: M 28 THR cc_start: 0.9001 (m) cc_final: 0.8682 (p) REVERT: M 43 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8433 (mmmt) REVERT: M 72 ASP cc_start: 0.7694 (t0) cc_final: 0.7424 (t0) REVERT: N 60 ASP cc_start: 0.8123 (p0) cc_final: 0.7101 (t0) REVERT: N 83 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7777 (mm-30) REVERT: N 94 ARG cc_start: 0.5915 (mpt180) cc_final: 0.4720 (tpt170) REVERT: I 82 MET cc_start: 0.8078 (mtm) cc_final: 0.7802 (mtm) REVERT: J 26 THR cc_start: 0.8128 (t) cc_final: 0.7887 (t) REVERT: J 27 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: J 31 ASN cc_start: 0.8902 (m-40) cc_final: 0.8690 (m-40) REVERT: J 94 ARG cc_start: 0.6257 (mpt180) cc_final: 0.4654 (mtp85) outliers start: 50 outliers final: 30 residues processed: 262 average time/residue: 0.3894 time to fit residues: 152.7564 Evaluate side-chains 245 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 197 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 105 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.064663 restraints weight = 51865.886| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.38 r_work: 0.2850 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21751 Z= 0.174 Angle : 0.609 13.307 29691 Z= 0.298 Chirality : 0.046 0.426 3549 Planarity : 0.004 0.034 3610 Dihedral : 6.343 59.852 4753 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.20 % Rotamer: Outliers : 2.09 % Allowed : 8.05 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % 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: 0.42 (0.17), residues: 2497 helix: 2.03 (0.28), residues: 384 sheet: 0.82 (0.19), residues: 764 loop : -0.56 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 36 HIS 0.005 0.001 HIS C 105 PHE 0.023 0.002 PHE C 53 TYR 0.035 0.001 TYR N 91 ARG 0.003 0.000 ARG L 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 63) link_NAG-ASN : angle 2.19674 ( 189) link_ALPHA1-6 : bond 0.00204 ( 2) link_ALPHA1-6 : angle 1.66909 ( 6) link_BETA1-4 : bond 0.00481 ( 21) link_BETA1-4 : angle 1.87756 ( 63) link_ALPHA1-3 : bond 0.00928 ( 6) link_ALPHA1-3 : angle 2.28961 ( 18) hydrogen bonds : bond 0.04185 ( 590) hydrogen bonds : angle 4.33167 ( 1521) link_BETA1-6 : bond 0.00356 ( 6) link_BETA1-6 : angle 1.31752 ( 18) SS BOND : bond 0.00350 ( 37) SS BOND : angle 0.82985 ( 74) covalent geometry : bond 0.00407 (21616) covalent geometry : angle 0.57419 (29323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 2.407 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: A 143 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7815 (mtm-85) REVERT: A 184 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7907 (ttp) REVERT: K 72 ASP cc_start: 0.8290 (t0) cc_final: 0.7686 (t70) REVERT: G 103 ARG cc_start: 0.8319 (tpp-160) cc_final: 0.7977 (mtp85) REVERT: L 33 TYR cc_start: 0.8024 (m-80) cc_final: 0.7542 (m-10) REVERT: L 49 ILE cc_start: 0.8767 (mp) cc_final: 0.8135 (tt) REVERT: L 54 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7374 (mtp85) REVERT: L 90 ARG cc_start: 0.8378 (ttm-80) cc_final: 0.7972 (ttm-80) REVERT: H 3 GLN cc_start: 0.7428 (pm20) cc_final: 0.7128 (pm20) REVERT: H 46 GLU cc_start: 0.8266 (tt0) cc_final: 0.7970 (tt0) REVERT: H 47 TRP cc_start: 0.7152 (t60) cc_final: 0.6893 (t60) REVERT: H 66 ARG cc_start: 0.7727 (mtm110) cc_final: 0.7460 (ptp-170) REVERT: H 79 TYR cc_start: 0.7677 (m-80) cc_final: 0.7256 (m-80) REVERT: C 207 LYS cc_start: 0.8682 (pttt) cc_final: 0.8278 (tmtt) REVERT: D 654 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: M 19 LYS cc_start: 0.8972 (tttt) cc_final: 0.8752 (tttp) REVERT: M 43 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8561 (mmmt) REVERT: M 72 ASP cc_start: 0.7658 (t0) cc_final: 0.7355 (t0) REVERT: N 60 ASP cc_start: 0.8126 (p0) cc_final: 0.7052 (t0) REVERT: N 83 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7705 (mm-30) REVERT: N 94 ARG cc_start: 0.5936 (mpt180) cc_final: 0.4805 (tpt170) REVERT: E 430 ILE cc_start: 0.9006 (mp) cc_final: 0.8726 (mm) REVERT: F 533 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8732 (mtp) REVERT: I 3 GLN cc_start: 0.8574 (mt0) cc_final: 0.8177 (mm-40) REVERT: I 13 GLN cc_start: 0.9108 (pm20) cc_final: 0.8898 (pm20) REVERT: I 82 MET cc_start: 0.8122 (mtm) cc_final: 0.7783 (mtm) REVERT: J 27 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: J 31 ASN cc_start: 0.8904 (m-40) cc_final: 0.8531 (m110) REVERT: J 94 ARG cc_start: 0.6288 (mpt180) cc_final: 0.4814 (mtp85) outliers start: 46 outliers final: 24 residues processed: 251 average time/residue: 0.3768 time to fit residues: 141.0686 Evaluate side-chains 233 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 27 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 131 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 3 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN E 99 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.090026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.065968 restraints weight = 51700.555| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.40 r_work: 0.2879 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21751 Z= 0.113 Angle : 0.567 14.509 29691 Z= 0.276 Chirality : 0.044 0.386 3549 Planarity : 0.003 0.031 3610 Dihedral : 5.830 56.075 4753 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.44 % Rotamer: Outliers : 1.86 % Allowed : 8.64 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % 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: 0.52 (0.17), residues: 2497 helix: 2.21 (0.28), residues: 384 sheet: 0.88 (0.19), residues: 764 loop : -0.53 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 36 HIS 0.004 0.001 HIS C 105 PHE 0.022 0.001 PHE C 53 TYR 0.025 0.001 TYR N 91 ARG 0.005 0.000 ARG L 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 63) link_NAG-ASN : angle 2.33601 ( 189) link_ALPHA1-6 : bond 0.00318 ( 2) link_ALPHA1-6 : angle 1.52267 ( 6) link_BETA1-4 : bond 0.00486 ( 21) link_BETA1-4 : angle 1.74522 ( 63) link_ALPHA1-3 : bond 0.00920 ( 6) link_ALPHA1-3 : angle 2.22112 ( 18) hydrogen bonds : bond 0.03648 ( 590) hydrogen bonds : angle 4.14417 ( 1521) link_BETA1-6 : bond 0.00404 ( 6) link_BETA1-6 : angle 1.31814 ( 18) SS BOND : bond 0.00290 ( 37) SS BOND : angle 0.73064 ( 74) covalent geometry : bond 0.00252 (21616) covalent geometry : angle 0.52692 (29323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 3.361 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: A 53 PHE cc_start: 0.8149 (p90) cc_final: 0.7909 (p90) REVERT: A 143 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7893 (mtm-85) REVERT: A 184 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7546 (ptm) REVERT: K 72 ASP cc_start: 0.8249 (t0) cc_final: 0.7644 (t70) REVERT: G 103 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.7984 (mtp85) REVERT: L 33 TYR cc_start: 0.7886 (m-80) cc_final: 0.7482 (m-10) REVERT: L 54 ARG cc_start: 0.7623 (mtp85) cc_final: 0.7277 (mtp85) REVERT: L 80 GLU cc_start: 0.6071 (mp0) cc_final: 0.5735 (mp0) REVERT: H 46 GLU cc_start: 0.8234 (tt0) cc_final: 0.7901 (tt0) REVERT: H 66 ARG cc_start: 0.7670 (mtm110) cc_final: 0.7434 (ptp-170) REVERT: H 79 TYR cc_start: 0.7972 (m-10) cc_final: 0.7710 (m-10) REVERT: C 207 LYS cc_start: 0.8768 (pttt) cc_final: 0.8344 (tmtt) REVERT: D 601 LYS cc_start: 0.9237 (ptpt) cc_final: 0.9036 (ptmt) REVERT: M 19 LYS cc_start: 0.8955 (tttt) cc_final: 0.8750 (tttp) REVERT: M 28 THR cc_start: 0.8930 (m) cc_final: 0.8700 (p) REVERT: M 43 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8539 (mmmt) REVERT: M 72 ASP cc_start: 0.7584 (t0) cc_final: 0.7237 (t0) REVERT: N 60 ASP cc_start: 0.8085 (p0) cc_final: 0.7047 (t0) REVERT: N 83 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7674 (mm-30) REVERT: N 94 ARG cc_start: 0.5773 (mpt180) cc_final: 0.4692 (tpt170) REVERT: E 430 ILE cc_start: 0.9000 (mp) cc_final: 0.8727 (mm) REVERT: E 475 MET cc_start: 0.8615 (mmt) cc_final: 0.8339 (tpp) REVERT: I 3 GLN cc_start: 0.8533 (mt0) cc_final: 0.8224 (mm-40) REVERT: I 82 MET cc_start: 0.8093 (mtm) cc_final: 0.7882 (mtm) REVERT: J 27 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: J 31 ASN cc_start: 0.8887 (m-40) cc_final: 0.8518 (m110) REVERT: J 94 ARG cc_start: 0.6271 (mpt180) cc_final: 0.4814 (mtp85) outliers start: 41 outliers final: 27 residues processed: 250 average time/residue: 0.4751 time to fit residues: 183.6821 Evaluate side-chains 244 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 662 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 27 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 22 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 227 optimal weight: 0.0050 chunk 211 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 240 optimal weight: 0.0870 chunk 222 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 overall best weight: 0.7174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** E 195 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 = 0.3477 r_free = 0.3477 target = 0.090271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.066232 restraints weight = 51662.390| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.41 r_work: 0.2889 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21751 Z= 0.106 Angle : 0.560 12.994 29691 Z= 0.274 Chirality : 0.044 0.412 3549 Planarity : 0.003 0.031 3610 Dihedral : 5.571 53.240 4751 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.44 % Rotamer: Outliers : 1.68 % Allowed : 9.05 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % 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: 0.55 (0.17), residues: 2497 helix: 2.29 (0.28), residues: 384 sheet: 0.86 (0.19), residues: 773 loop : -0.50 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 PHE 0.021 0.001 PHE C 53 TYR 0.028 0.001 TYR N 91 ARG 0.003 0.000 ARG L 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 63) link_NAG-ASN : angle 2.18471 ( 189) link_ALPHA1-6 : bond 0.00413 ( 2) link_ALPHA1-6 : angle 1.47819 ( 6) link_BETA1-4 : bond 0.00484 ( 21) link_BETA1-4 : angle 1.69875 ( 63) link_ALPHA1-3 : bond 0.00912 ( 6) link_ALPHA1-3 : angle 2.15578 ( 18) hydrogen bonds : bond 0.03506 ( 590) hydrogen bonds : angle 4.03365 ( 1521) link_BETA1-6 : bond 0.00414 ( 6) link_BETA1-6 : angle 1.33829 ( 18) SS BOND : bond 0.00408 ( 37) SS BOND : angle 0.87856 ( 74) covalent geometry : bond 0.00234 (21616) covalent geometry : angle 0.52364 (29323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8227 (ttm110) cc_final: 0.8006 (ttm-80) REVERT: A 173 TYR cc_start: 0.8443 (p90) cc_final: 0.8100 (p90) REVERT: A 184 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7579 (ptm) REVERT: K 72 ASP cc_start: 0.8241 (t0) cc_final: 0.7634 (t70) REVERT: K 86 ASP cc_start: 0.8238 (m-30) cc_final: 0.8018 (m-30) REVERT: G 103 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7974 (mtp85) REVERT: L 33 TYR cc_start: 0.7835 (m-80) cc_final: 0.7450 (m-10) REVERT: L 36 TRP cc_start: 0.7868 (m100) cc_final: 0.7613 (m100) REVERT: L 49 ILE cc_start: 0.8833 (mp) cc_final: 0.8321 (tt) REVERT: L 54 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7410 (mtp85) REVERT: H 3 GLN cc_start: 0.7419 (pm20) cc_final: 0.7101 (pm20) REVERT: H 46 GLU cc_start: 0.8177 (tt0) cc_final: 0.7860 (tt0) REVERT: H 79 TYR cc_start: 0.7990 (m-10) cc_final: 0.7758 (m-10) REVERT: C 207 LYS cc_start: 0.8746 (pttt) cc_final: 0.8306 (tmtt) REVERT: D 601 LYS cc_start: 0.9230 (ptpt) cc_final: 0.9028 (ptmt) REVERT: M 28 THR cc_start: 0.8913 (m) cc_final: 0.8675 (p) REVERT: M 72 ASP cc_start: 0.7581 (t0) cc_final: 0.7232 (t0) REVERT: N 60 ASP cc_start: 0.8064 (p0) cc_final: 0.7046 (t0) REVERT: N 83 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7786 (mm-30) REVERT: N 94 ARG cc_start: 0.5866 (mpt180) cc_final: 0.4872 (tpt170) REVERT: E 430 ILE cc_start: 0.8991 (mp) cc_final: 0.8723 (mm) REVERT: E 475 MET cc_start: 0.8627 (mmt) cc_final: 0.8377 (tpp) REVERT: I 3 GLN cc_start: 0.8552 (mt0) cc_final: 0.8266 (mm-40) REVERT: I 82 MET cc_start: 0.8107 (mtm) cc_final: 0.7850 (mtm) REVERT: J 27 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: J 31 ASN cc_start: 0.8862 (m-40) cc_final: 0.8490 (m110) REVERT: J 94 ARG cc_start: 0.6275 (mpt180) cc_final: 0.4809 (mtp85) outliers start: 37 outliers final: 29 residues processed: 254 average time/residue: 0.3712 time to fit residues: 141.8844 Evaluate side-chains 243 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 662 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 150 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 235 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 162 optimal weight: 0.4980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 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 = 0.3469 r_free = 0.3469 target = 0.089743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.065788 restraints weight = 51625.909| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.37 r_work: 0.2878 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21751 Z= 0.133 Angle : 0.701 47.300 29691 Z= 0.373 Chirality : 0.044 0.353 3549 Planarity : 0.004 0.054 3610 Dihedral : 5.447 51.978 4751 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 1.91 % Allowed : 9.05 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % 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: 0.54 (0.17), residues: 2497 helix: 2.29 (0.28), residues: 384 sheet: 0.86 (0.19), residues: 773 loop : -0.51 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 PHE 0.026 0.001 PHE C 53 TYR 0.027 0.001 TYR N 91 ARG 0.005 0.000 ARG L 90 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 63) link_NAG-ASN : angle 2.52669 ( 189) link_ALPHA1-6 : bond 0.00310 ( 2) link_ALPHA1-6 : angle 1.49854 ( 6) link_BETA1-4 : bond 0.00459 ( 21) link_BETA1-4 : angle 1.72143 ( 63) link_ALPHA1-3 : bond 0.00852 ( 6) link_ALPHA1-3 : angle 2.17340 ( 18) hydrogen bonds : bond 0.03595 ( 590) hydrogen bonds : angle 4.06692 ( 1521) link_BETA1-6 : bond 0.00392 ( 6) link_BETA1-6 : angle 1.38326 ( 18) SS BOND : bond 0.00382 ( 37) SS BOND : angle 0.84488 ( 74) covalent geometry : bond 0.00309 (21616) covalent geometry : angle 0.66640 (29323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7980 (ttm-80) REVERT: A 184 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7635 (ptm) REVERT: K 72 ASP cc_start: 0.8227 (t0) cc_final: 0.7624 (t70) REVERT: G 103 ARG cc_start: 0.8310 (tpp-160) cc_final: 0.8019 (mtp85) REVERT: L 33 TYR cc_start: 0.7839 (m-80) cc_final: 0.7448 (m-10) REVERT: L 36 TRP cc_start: 0.7862 (m100) cc_final: 0.7637 (m100) REVERT: L 49 ILE cc_start: 0.8843 (mp) cc_final: 0.8350 (tt) REVERT: L 72 PHE cc_start: 0.6985 (m-10) cc_final: 0.6680 (m-10) REVERT: H 3 GLN cc_start: 0.7397 (pm20) cc_final: 0.7075 (pm20) REVERT: H 46 GLU cc_start: 0.8138 (tt0) cc_final: 0.7851 (tt0) REVERT: H 79 TYR cc_start: 0.8038 (m-10) cc_final: 0.7824 (m-10) REVERT: C 207 LYS cc_start: 0.8744 (pttt) cc_final: 0.8309 (tmtt) REVERT: M 28 THR cc_start: 0.8920 (m) cc_final: 0.8671 (p) REVERT: M 72 ASP cc_start: 0.7578 (t0) cc_final: 0.7230 (t0) REVERT: N 60 ASP cc_start: 0.8079 (p0) cc_final: 0.7067 (t0) REVERT: N 83 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7704 (mm-30) REVERT: N 94 ARG cc_start: 0.5926 (mpt180) cc_final: 0.4838 (tpt170) REVERT: E 430 ILE cc_start: 0.9022 (mp) cc_final: 0.8743 (mm) REVERT: I 3 GLN cc_start: 0.8620 (mt0) cc_final: 0.8338 (mm-40) REVERT: I 82 MET cc_start: 0.8124 (mtm) cc_final: 0.7817 (mtm) REVERT: J 27 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: J 31 ASN cc_start: 0.8865 (m-40) cc_final: 0.8488 (m110) REVERT: J 94 ARG cc_start: 0.6323 (mpt180) cc_final: 0.4826 (mtp85) outliers start: 42 outliers final: 32 residues processed: 237 average time/residue: 0.3740 time to fit residues: 132.8088 Evaluate side-chains 243 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 662 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 92 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 152 optimal weight: 0.0170 chunk 7 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 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 = 0.3447 r_free = 0.3447 target = 0.088501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064442 restraints weight = 52018.378| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.38 r_work: 0.2846 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 21751 Z= 0.203 Angle : 0.640 16.428 29691 Z= 0.315 Chirality : 0.048 0.776 3549 Planarity : 0.004 0.070 3610 Dihedral : 5.806 54.589 4751 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.16 % Favored : 95.67 % Rotamer: Outliers : 2.14 % Allowed : 9.09 % Favored : 88.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % 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: 0.45 (0.17), residues: 2497 helix: 2.18 (0.28), residues: 384 sheet: 0.80 (0.19), residues: 773 loop : -0.56 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.005 0.001 HIS C 105 PHE 0.026 0.002 PHE C 53 TYR 0.028 0.001 TYR N 91 ARG 0.012 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 63) link_NAG-ASN : angle 2.32097 ( 189) link_ALPHA1-6 : bond 0.00268 ( 2) link_ALPHA1-6 : angle 1.42264 ( 6) link_BETA1-4 : bond 0.00471 ( 21) link_BETA1-4 : angle 1.78934 ( 63) link_ALPHA1-3 : bond 0.00861 ( 6) link_ALPHA1-3 : angle 2.26112 ( 18) hydrogen bonds : bond 0.04069 ( 590) hydrogen bonds : angle 4.18294 ( 1521) link_BETA1-6 : bond 0.00349 ( 6) link_BETA1-6 : angle 1.41476 ( 18) SS BOND : bond 0.00429 ( 37) SS BOND : angle 0.92898 ( 74) covalent geometry : bond 0.00478 (21616) covalent geometry : angle 0.60565 (29323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8241 (ttm110) cc_final: 0.8012 (ttm-80) REVERT: A 184 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7814 (ptm) REVERT: K 72 ASP cc_start: 0.8295 (t0) cc_final: 0.7709 (t70) REVERT: G 103 ARG cc_start: 0.8326 (tpp-160) cc_final: 0.8009 (mtp85) REVERT: L 33 TYR cc_start: 0.7926 (m-80) cc_final: 0.7495 (m-10) REVERT: L 36 TRP cc_start: 0.7842 (m100) cc_final: 0.7628 (m100) REVERT: L 49 ILE cc_start: 0.8807 (mp) cc_final: 0.8264 (tt) REVERT: L 54 ARG cc_start: 0.7734 (mtp85) cc_final: 0.7336 (mtp85) REVERT: L 72 PHE cc_start: 0.6925 (m-10) cc_final: 0.6636 (m-10) REVERT: H 3 GLN cc_start: 0.7371 (pm20) cc_final: 0.7046 (pm20) REVERT: H 79 TYR cc_start: 0.7995 (m-10) cc_final: 0.7780 (m-10) REVERT: C 207 LYS cc_start: 0.8744 (pttt) cc_final: 0.8328 (tmtt) REVERT: M 28 THR cc_start: 0.8975 (m) cc_final: 0.8714 (p) REVERT: M 72 ASP cc_start: 0.7692 (t0) cc_final: 0.7357 (t0) REVERT: N 60 ASP cc_start: 0.8215 (p0) cc_final: 0.7198 (t0) REVERT: N 83 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7649 (mm-30) REVERT: N 94 ARG cc_start: 0.6009 (mpt180) cc_final: 0.4784 (tpt170) REVERT: F 533 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8765 (mtp) REVERT: I 3 GLN cc_start: 0.8619 (mt0) cc_final: 0.8344 (mm-40) REVERT: I 82 MET cc_start: 0.8146 (mtm) cc_final: 0.7711 (mtm) REVERT: J 27 ASP cc_start: 0.7865 (m-30) cc_final: 0.7571 (m-30) REVERT: J 31 ASN cc_start: 0.8878 (m-40) cc_final: 0.8492 (m110) REVERT: J 94 ARG cc_start: 0.6446 (mpt180) cc_final: 0.5340 (mmt180) outliers start: 47 outliers final: 32 residues processed: 240 average time/residue: 0.3913 time to fit residues: 140.5395 Evaluate side-chains 238 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 117 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 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 = 0.3436 r_free = 0.3436 target = 0.087874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.063807 restraints weight = 51980.682| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.36 r_work: 0.2831 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21751 Z= 0.219 Angle : 0.664 15.775 29691 Z= 0.323 Chirality : 0.047 0.607 3549 Planarity : 0.004 0.049 3610 Dihedral : 6.358 62.866 4751 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.33 % Favored : 95.51 % Rotamer: Outliers : 1.77 % Allowed : 9.45 % Favored : 88.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % 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: 0.28 (0.17), residues: 2497 helix: 2.03 (0.28), residues: 384 sheet: 0.72 (0.19), residues: 767 loop : -0.68 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 103 HIS 0.005 0.001 HIS C 105 PHE 0.024 0.002 PHE C 53 TYR 0.027 0.001 TYR N 91 ARG 0.009 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 63) link_NAG-ASN : angle 2.41978 ( 189) link_ALPHA1-6 : bond 0.00180 ( 2) link_ALPHA1-6 : angle 1.56788 ( 6) link_BETA1-4 : bond 0.00446 ( 21) link_BETA1-4 : angle 1.82526 ( 63) link_ALPHA1-3 : bond 0.00853 ( 6) link_ALPHA1-3 : angle 2.17203 ( 18) hydrogen bonds : bond 0.04319 ( 590) hydrogen bonds : angle 4.35548 ( 1521) link_BETA1-6 : bond 0.00364 ( 6) link_BETA1-6 : angle 1.60631 ( 18) SS BOND : bond 0.00441 ( 37) SS BOND : angle 0.98143 ( 74) covalent geometry : bond 0.00519 (21616) covalent geometry : angle 0.62767 (29323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8257 (ttm110) cc_final: 0.8037 (ttm110) REVERT: A 184 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7890 (ptm) REVERT: K 43 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7901 (pttp) REVERT: K 72 ASP cc_start: 0.8344 (t0) cc_final: 0.7757 (t70) REVERT: G 103 ARG cc_start: 0.8328 (tpp-160) cc_final: 0.7959 (mtp85) REVERT: L 33 TYR cc_start: 0.7951 (m-80) cc_final: 0.7538 (m-10) REVERT: L 37 TYR cc_start: 0.7526 (m-80) cc_final: 0.7080 (m-80) REVERT: L 49 ILE cc_start: 0.8826 (mp) cc_final: 0.8290 (tt) REVERT: L 54 ARG cc_start: 0.7782 (mtp85) cc_final: 0.7400 (mtp85) REVERT: L 62 ARG cc_start: 0.5197 (OUTLIER) cc_final: 0.4767 (ttm170) REVERT: L 72 PHE cc_start: 0.6946 (m-10) cc_final: 0.6672 (m-10) REVERT: H 3 GLN cc_start: 0.7393 (pm20) cc_final: 0.7069 (pm20) REVERT: H 79 TYR cc_start: 0.7991 (m-10) cc_final: 0.7787 (m-10) REVERT: C 207 LYS cc_start: 0.8759 (pttt) cc_final: 0.8343 (tmtt) REVERT: D 624 ASP cc_start: 0.8686 (m-30) cc_final: 0.8318 (m-30) REVERT: M 28 THR cc_start: 0.8992 (m) cc_final: 0.8724 (p) REVERT: M 72 ASP cc_start: 0.7710 (t0) cc_final: 0.7372 (t0) REVERT: N 60 ASP cc_start: 0.8253 (p0) cc_final: 0.7249 (t0) REVERT: N 83 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7651 (mm-30) REVERT: N 94 ARG cc_start: 0.6092 (mpt180) cc_final: 0.4681 (tpt170) REVERT: F 533 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8800 (mtp) REVERT: I 3 GLN cc_start: 0.8659 (mt0) cc_final: 0.8382 (mm-40) REVERT: I 82 MET cc_start: 0.8186 (mtm) cc_final: 0.7778 (mtm) REVERT: J 27 ASP cc_start: 0.7831 (m-30) cc_final: 0.7553 (m-30) REVERT: J 31 ASN cc_start: 0.8890 (m-40) cc_final: 0.8680 (m110) REVERT: J 94 ARG cc_start: 0.6499 (mpt180) cc_final: 0.5375 (mmt180) outliers start: 39 outliers final: 32 residues processed: 237 average time/residue: 0.3709 time to fit residues: 130.4863 Evaluate side-chains 237 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 82 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 232 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 41 optimal weight: 0.2980 chunk 200 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 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 = 0.3456 r_free = 0.3456 target = 0.089006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065355 restraints weight = 51312.966| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.31 r_work: 0.2850 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21751 Z= 0.154 Angle : 0.613 18.623 29691 Z= 0.299 Chirality : 0.045 0.370 3549 Planarity : 0.004 0.032 3610 Dihedral : 6.413 110.545 4751 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.00 % Favored : 95.84 % Rotamer: Outliers : 1.64 % Allowed : 9.77 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % 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: 0.35 (0.17), residues: 2497 helix: 2.15 (0.28), residues: 384 sheet: 0.95 (0.20), residues: 728 loop : -0.74 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP L 36 HIS 0.004 0.001 HIS C 105 PHE 0.025 0.001 PHE C 53 TYR 0.026 0.001 TYR N 91 ARG 0.008 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 63) link_NAG-ASN : angle 2.50967 ( 189) link_ALPHA1-6 : bond 0.00354 ( 2) link_ALPHA1-6 : angle 1.50563 ( 6) link_BETA1-4 : bond 0.00462 ( 21) link_BETA1-4 : angle 1.70826 ( 63) link_ALPHA1-3 : bond 0.00885 ( 6) link_ALPHA1-3 : angle 2.15953 ( 18) hydrogen bonds : bond 0.03907 ( 590) hydrogen bonds : angle 4.22476 ( 1521) link_BETA1-6 : bond 0.00362 ( 6) link_BETA1-6 : angle 1.44721 ( 18) SS BOND : bond 0.00398 ( 37) SS BOND : angle 0.89730 ( 74) covalent geometry : bond 0.00362 (21616) covalent geometry : angle 0.57134 (29323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10619.19 seconds wall clock time: 186 minutes 15.69 seconds (11175.69 seconds total)