Starting phenix.real_space_refine on Sat Jul 4 14:11:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t74_25733/07_2026/7t74_25733.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t74_25733/07_2026/7t74_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 { model { file = "/net/cci-nas-00/data/ceres_data/7t74_25733/07_2026/7t74_25733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t74_25733/07_2026/7t74_25733.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7t74_25733/07_2026/7t74_25733.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t74_25733/07_2026/7t74_25733.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t74_25733/07_2026/7t74_25733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t74_25733/07_2026/7t74_25733.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 4.11, per 1000 atoms: 0.19 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: 1.94 Conformation dependent library (CDL) restraints added in 693.3 milliseconds 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: 0.52 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: 3.43 Time building geometry restraints manager: 2.42 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 - 17.98: 11614 17.98 - 35.96: 336 35.96 - 53.95: 105 53.95 - 71.93: 33 71.93 - 89.91: 17 Dihedral angle restraints: 12105 sinusoidal: 4818 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 12102 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.410 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 10.634 89.911 7332 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 ARG 0.010 0.001 ARG K 71 TYR 0.049 0.007 TYR J 96 PHE 0.034 0.006 PHE E 353 TRP 0.061 0.009 TRP C 96 HIS 0.012 0.003 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.02239 / 1.18 (21616) covalent geometry : angle 1.77186 / 1.13 (29323) SS BOND : bond 0.00884 / 0.51 ( 37) SS BOND : angle 2.55441 / 1.73 ( 74) hydrogen bonds : bond 0.16605 / 10.81 ( 590) hydrogen bonds : angle 6.64191 / 4.60 ( 1521) link_ALPHA1-3 : bond 0.06562 / 3.58 ( 6) link_ALPHA1-3 : angle 4.16153 / 2.56 ( 18) link_ALPHA1-6 : bond 0.00814 / 0.43 ( 2) link_ALPHA1-6 : angle 1.64499 / 1.09 ( 6) link_BETA1-4 : bond 0.06176 / 3.81 ( 21) link_BETA1-4 : angle 4.53813 / 3.20 ( 63) link_BETA1-6 : bond 0.07806 / 4.13 ( 6) link_BETA1-6 : angle 4.25299 / 2.37 ( 18) link_NAG-ASN : bond 0.07559 / 4.74 ( 63) link_NAG-ASN : angle 2.83916 / 1.94 ( 189) *********************** 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 : 0.742 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: 0.8339 (p) REVERT: G 24 THR cc_start: 0.8937 (m) cc_final: 0.8521 (p) REVERT: G 47 MET cc_start: 0.8398 (mmm) cc_final: 0.8167 (mmm) REVERT: L 34 PHE cc_start: 0.7476 (t80) cc_final: 0.7138 (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: 0.5153 (tp) REVERT: L 96 PHE cc_start: 0.4907 (m-80) cc_final: 0.4673 (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: 0.6927 (tp) REVERT: H 82 MET cc_start: 0.6262 (mtm) cc_final: 0.5895 (mtm) REVERT: H 93 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5429 (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: 0.8830 (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: 0.6475 (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: 0.8921 (pt) outliers start: 14 outliers final: 4 residues processed: 417 average time/residue: 0.1588 time to fit residues: 96.9699 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 : 0.537 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 6 GLN C 187 ASN N 6 GLN N 79 GLN F 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.092535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068457 restraints weight = 51219.921| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.40 r_work: 0.2938 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21751 Z= 0.157 Angle : 0.729 17.527 29691 Z= 0.359 Chirality : 0.048 0.648 3549 Planarity : 0.004 0.051 3610 Dihedral : 5.306 51.635 2755 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.00 % Rotamer: Outliers : 1.77 % Allowed : 5.41 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 2497 helix: 1.95 (0.27), residues: 378 sheet: 0.70 (0.18), residues: 838 loop : -0.07 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 588 TYR 0.019 0.001 TYR C 173 PHE 0.022 0.002 PHE C 53 TRP 0.026 0.001 TRP E 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (21616) covalent geometry : angle 0.68255 / 0.35 (29323) SS BOND : bond 0.00268 / 0.18 ( 37) SS BOND : angle 0.90001 / 0.58 ( 74) hydrogen bonds : bond 0.05284 / 3.44 ( 590) hydrogen bonds : angle 4.95761 / 3.41 ( 1521) link_ALPHA1-3 : bond 0.00770 / 0.41 ( 6) link_ALPHA1-3 : angle 1.90446 / 1.31 ( 18) link_ALPHA1-6 : bond 0.00276 / 0.13 ( 2) link_ALPHA1-6 : angle 1.65314 / 1.15 ( 6) link_BETA1-4 : bond 0.00676 / 0.39 ( 21) link_BETA1-4 : angle 2.64463 / 1.80 ( 63) link_BETA1-6 : bond 0.00685 / 0.32 ( 6) link_BETA1-6 : angle 1.16410 / 0.60 ( 18) link_NAG-ASN : bond 0.00471 / 0.28 ( 63) link_NAG-ASN : angle 2.80874 / 1.81 ( 189) *********************** 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 333 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 294 time to evaluate : 0.788 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: K 34 MET cc_start: 0.8751 (mtt) cc_final: 0.8529 (mtm) REVERT: K 72 ASP cc_start: 0.8018 (t0) cc_final: 0.7531 (t70) REVERT: G 5 THR cc_start: 0.8714 (m) cc_final: 0.8330 (p) REVERT: G 24 THR cc_start: 0.9239 (m) cc_final: 0.8644 (p) REVERT: G 47 MET cc_start: 0.8608 (mmm) cc_final: 0.8195 (mmt) REVERT: L 13 LEU cc_start: 0.7011 (mt) cc_final: 0.6697 (mp) REVERT: L 33 TYR cc_start: 0.7663 (m-80) cc_final: 0.7341 (m-80) REVERT: L 34 PHE cc_start: 0.7276 (t80) cc_final: 0.6874 (t80) REVERT: L 36 TRP cc_start: 0.7640 (m100) cc_final: 0.7416 (m100) REVERT: L 54 ARG cc_start: 0.7720 (mtp85) cc_final: 0.7481 (mtp85) REVERT: L 63 PHE cc_start: 0.7858 (m-80) cc_final: 0.7198 (m-80) REVERT: H 46 GLU cc_start: 0.8090 (tt0) cc_final: 0.7564 (tt0) REVERT: H 79 TYR cc_start: 0.7564 (m-10) cc_final: 0.7319 (m-10) REVERT: H 82 LEU cc_start: 0.5700 (mp) cc_final: 0.5449 (pp) REVERT: H 93 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6940 (ppp) REVERT: C 207 LYS cc_start: 0.8811 (pttt) cc_final: 0.8356 (tmtt) REVERT: D 624 ASP cc_start: 0.9099 (m-30) cc_final: 0.8546 (m-30) REVERT: M 28 THR cc_start: 0.8719 (m) cc_final: 0.8277 (p) REVERT: M 43 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8240 (mmmt) REVERT: M 72 ASP cc_start: 0.7682 (t0) cc_final: 0.7474 (t0) REVERT: M 83 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6685 (mpp80) REVERT: M 110 THR cc_start: 0.8901 (m) cc_final: 0.8667 (t) REVERT: N 60 ASP cc_start: 0.8191 (p0) cc_final: 0.6809 (t0) REVERT: N 83 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7513 (mm-30) REVERT: N 91 TYR cc_start: 0.9146 (t80) cc_final: 0.8892 (t80) REVERT: N 94 ARG cc_start: 0.5577 (mpt180) cc_final: 0.4269 (mmt180) REVERT: F 571 TRP cc_start: 0.7255 (t-100) cc_final: 0.7002 (t60) REVERT: I 82 MET cc_start: 0.7918 (mtm) cc_final: 0.7485 (mtm) REVERT: J 31 ASN cc_start: 0.8674 (m-40) cc_final: 0.8342 (m110) REVERT: J 94 ARG cc_start: 0.5633 (mpt180) cc_final: 0.4559 (mtp85) outliers start: 39 outliers final: 16 residues processed: 316 average time/residue: 0.1512 time to fit residues: 71.0585 Evaluate side-chains 239 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 M residue 83 ARG 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 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.090710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.066294 restraints weight = 51982.773| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.49 r_work: 0.2881 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21751 Z= 0.168 Angle : 0.662 22.503 29691 Z= 0.323 Chirality : 0.047 0.637 3549 Planarity : 0.004 0.035 3610 Dihedral : 4.798 42.218 2750 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.56 % Rotamer: Outliers : 2.23 % Allowed : 6.64 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.17), residues: 2497 helix: 2.15 (0.28), residues: 384 sheet: 0.73 (0.18), residues: 792 loop : -0.27 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 143 TYR 0.014 0.001 TYR C 173 PHE 0.030 0.002 PHE L 96 TRP 0.026 0.001 TRP H 47 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (21616) covalent geometry : angle 0.61626 / 0.31 (29323) SS BOND : bond 0.00345 / 0.22 ( 37) SS BOND : angle 0.88334 / 0.53 ( 74) hydrogen bonds : bond 0.04494 / 2.92 ( 590) hydrogen bonds : angle 4.56537 / 3.13 ( 1521) link_ALPHA1-3 : bond 0.00550 / 0.28 ( 6) link_ALPHA1-3 : angle 2.03322 / 1.49 ( 18) link_ALPHA1-6 : bond 0.00221 / 0.11 ( 2) link_ALPHA1-6 : angle 1.57404 / 1.12 ( 6) link_BETA1-4 : bond 0.00543 / 0.31 ( 21) link_BETA1-4 : angle 1.94197 / 1.33 ( 63) link_BETA1-6 : bond 0.00423 / 0.24 ( 6) link_BETA1-6 : angle 1.13666 / 0.66 ( 18) link_NAG-ASN : bond 0.00751 / 0.41 ( 63) link_NAG-ASN : angle 2.77122 / 1.80 ( 189) *********************** 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 289 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 0.776 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: 0.8266 (OUTLIER) cc_final: 0.7701 (mmt90) REVERT: A 184 MET cc_start: 0.8050 (ttp) cc_final: 0.7723 (ttp) REVERT: K 4 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8114 (mm) REVERT: K 72 ASP cc_start: 0.8074 (t0) cc_final: 0.7473 (t70) REVERT: G 5 THR cc_start: 0.8774 (m) cc_final: 0.8436 (p) REVERT: G 47 MET cc_start: 0.8493 (mmm) cc_final: 0.8215 (mmt) REVERT: G 103 ARG cc_start: 0.8491 (tpp-160) cc_final: 0.8124 (tpt170) REVERT: L 13 LEU cc_start: 0.7270 (mt) cc_final: 0.7039 (mp) REVERT: L 33 TYR cc_start: 0.7720 (m-80) cc_final: 0.7418 (m-80) REVERT: L 54 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7391 (mtp85) REVERT: L 63 PHE cc_start: 0.7320 (m-80) cc_final: 0.6959 (m-80) REVERT: H 46 GLU cc_start: 0.8202 (tt0) cc_final: 0.7948 (tt0) REVERT: H 71 ARG cc_start: 0.6303 (ttm170) cc_final: 0.5833 (ttm170) REVERT: H 72 ASP cc_start: 0.7630 (p0) cc_final: 0.7248 (p0) REVERT: H 82 LEU cc_start: 0.5474 (mp) cc_final: 0.5066 (pp) REVERT: C 207 LYS cc_start: 0.8732 (pttt) cc_final: 0.8281 (tmtt) REVERT: D 624 ASP cc_start: 0.9030 (m-30) cc_final: 0.8321 (m-30) REVERT: D 654 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: M 19 LYS cc_start: 0.8671 (tttt) cc_final: 0.8177 (tttp) REVERT: M 28 THR cc_start: 0.8732 (m) cc_final: 0.8354 (p) REVERT: M 43 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8180 (mmmt) REVERT: M 72 ASP cc_start: 0.7722 (t0) cc_final: 0.7384 (t0) REVERT: M 110 THR cc_start: 0.8961 (m) cc_final: 0.8714 (t) REVERT: N 60 ASP cc_start: 0.8202 (p0) cc_final: 0.7012 (t0) REVERT: N 83 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7476 (mm-30) REVERT: N 94 ARG cc_start: 0.5584 (mpt180) cc_final: 0.4192 (mmt180) REVERT: E 187 ASN cc_start: 0.7129 (t0) cc_final: 0.6843 (m-40) REVERT: F 571 TRP cc_start: 0.7162 (t-100) cc_final: 0.6865 (t60) REVERT: I 82 MET cc_start: 0.8213 (mtm) cc_final: 0.7623 (mtm) REVERT: J 17 GLN cc_start: 0.7653 (mp10) cc_final: 0.7365 (pt0) REVERT: J 27 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: J 31 ASN cc_start: 0.8833 (m-40) cc_final: 0.8522 (m-40) REVERT: J 79 GLN cc_start: 0.6859 (mp10) cc_final: 0.6622 (mp-120) REVERT: J 94 ARG cc_start: 0.5963 (mpt180) cc_final: 0.4669 (mtp85) outliers start: 49 outliers final: 25 residues processed: 273 average time/residue: 0.1478 time to fit residues: 60.6216 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 : 0.684 ------------------------------------------------------------------------------- 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 143 ARG 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 26 THR 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 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 654 GLU Chi-restraints excluded: chain M residue 83 ARG 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 62 optimal weight: 10.0000 chunk 209 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 220 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 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 = 0.3479 r_free = 0.3479 target = 0.090267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066063 restraints weight = 52177.020| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.42 r_work: 0.2877 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21751 Z= 0.162 Angle : 0.635 21.673 29691 Z= 0.308 Chirality : 0.048 0.732 3549 Planarity : 0.004 0.035 3610 Dihedral : 4.625 36.322 2747 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 1.91 % Allowed : 7.27 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.17), residues: 2497 helix: 2.13 (0.28), residues: 384 sheet: 0.85 (0.19), residues: 774 loop : -0.42 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 64 TYR 0.029 0.001 TYR N 91 PHE 0.025 0.002 PHE C 53 TRP 0.015 0.001 TRP L 36 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (21616) covalent geometry : angle 0.58825 / 0.30 (29323) SS BOND : bond 0.00352 / 0.23 ( 37) SS BOND : angle 0.81779 / 0.49 ( 74) hydrogen bonds : bond 0.04214 / 2.73 ( 590) hydrogen bonds : angle 4.40708 / 3.02 ( 1521) link_ALPHA1-3 : bond 0.00462 / 0.24 ( 6) link_ALPHA1-3 : angle 1.95471 / 1.46 ( 18) link_ALPHA1-6 : bond 0.00228 / 0.12 ( 2) link_ALPHA1-6 : angle 1.59600 / 1.12 ( 6) link_BETA1-4 : bond 0.00458 / 0.26 ( 21) link_BETA1-4 : angle 1.84272 / 1.25 ( 63) link_BETA1-6 : bond 0.00301 / 0.15 ( 6) link_BETA1-6 : angle 1.23846 / 0.71 ( 18) link_NAG-ASN : bond 0.00615 / 0.29 ( 63) link_NAG-ASN : angle 2.76750 / 1.89 ( 189) *********************** 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 264 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7960 (mtm-85) REVERT: A 184 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7775 (ttp) REVERT: K 72 ASP cc_start: 0.8183 (t0) cc_final: 0.7579 (t70) REVERT: G 5 THR cc_start: 0.8783 (m) cc_final: 0.8579 (p) REVERT: G 6 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7224 (pt0) REVERT: G 47 MET cc_start: 0.8516 (mmm) cc_final: 0.8151 (mmt) REVERT: G 103 ARG cc_start: 0.8363 (tpp-160) cc_final: 0.8035 (mtp85) REVERT: L 13 LEU cc_start: 0.7289 (mt) cc_final: 0.7083 (mp) REVERT: L 33 TYR cc_start: 0.7835 (m-80) cc_final: 0.7581 (m-80) REVERT: L 54 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7439 (mtp85) REVERT: L 90 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.7912 (ttm-80) REVERT: H 38 ARG cc_start: 0.6953 (ptt-90) cc_final: 0.5992 (ptt90) REVERT: H 46 GLU cc_start: 0.8225 (tt0) cc_final: 0.7444 (mp0) REVERT: H 57 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6865 (mtpp) REVERT: H 64 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7646 (mtt-85) REVERT: H 66 ARG cc_start: 0.7515 (mtm110) cc_final: 0.6506 (ptm160) REVERT: H 82 LEU cc_start: 0.5426 (mp) cc_final: 0.5116 (pp) REVERT: C 207 LYS cc_start: 0.8626 (pttt) cc_final: 0.8209 (tmtt) REVERT: D 624 ASP cc_start: 0.9017 (m-30) cc_final: 0.8367 (m-30) REVERT: D 654 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: M 19 LYS cc_start: 0.8858 (tttt) cc_final: 0.8426 (tttp) REVERT: M 28 THR cc_start: 0.8877 (m) cc_final: 0.8530 (p) REVERT: M 43 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8319 (mmmt) REVERT: M 72 ASP cc_start: 0.7786 (t0) cc_final: 0.7422 (t0) REVERT: M 83 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6685 (mtm-85) REVERT: N 60 ASP cc_start: 0.8155 (p0) cc_final: 0.7025 (t0) REVERT: N 83 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7753 (mm-30) REVERT: N 94 ARG cc_start: 0.5564 (mpt180) cc_final: 0.4830 (tpt170) REVERT: E 187 ASN cc_start: 0.7149 (t0) cc_final: 0.6857 (m-40) REVERT: J 17 GLN cc_start: 0.7586 (mp10) cc_final: 0.7383 (pt0) REVERT: J 27 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: J 31 ASN cc_start: 0.8855 (m-40) cc_final: 0.8473 (m110) REVERT: J 94 ARG cc_start: 0.6112 (mpt180) cc_final: 0.4847 (mtp85) outliers start: 42 outliers final: 25 residues processed: 249 average time/residue: 0.1597 time to fit residues: 59.8890 Evaluate side-chains 243 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 143 ARG Chi-restraints excluded: chain A residue 184 MET 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 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 57 LYS 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 265 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain N residue 85 ASP 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 F residue 588 ARG Chi-restraints excluded: chain F residue 662 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 53 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 230 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN E 99 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.090382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.066309 restraints weight = 51930.673| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.40 r_work: 0.2883 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21751 Z= 0.139 Angle : 0.595 17.859 29691 Z= 0.288 Chirality : 0.045 0.487 3549 Planarity : 0.004 0.037 3610 Dihedral : 4.428 26.353 2747 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % Rotamer: Outliers : 1.73 % Allowed : 7.86 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2497 helix: 2.20 (0.28), residues: 384 sheet: 0.92 (0.19), residues: 760 loop : -0.45 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 40 TYR 0.023 0.001 TYR N 91 PHE 0.022 0.002 PHE C 53 TRP 0.030 0.001 TRP H 47 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21616) covalent geometry : angle 0.54836 / 0.28 (29323) SS BOND : bond 0.00322 / 0.20 ( 37) SS BOND : angle 0.78551 / 0.46 ( 74) hydrogen bonds : bond 0.03870 / 2.51 ( 590) hydrogen bonds : angle 4.28253 / 2.94 ( 1521) link_ALPHA1-3 : bond 0.00445 / 0.23 ( 6) link_ALPHA1-3 : angle 1.92238 / 1.45 ( 18) link_ALPHA1-6 : bond 0.00223 / 0.11 ( 2) link_ALPHA1-6 : angle 1.53966 / 1.08 ( 6) link_BETA1-4 : bond 0.00444 / 0.25 ( 21) link_BETA1-4 : angle 1.65772 / 1.12 ( 63) link_BETA1-6 : bond 0.00319 / 0.16 ( 6) link_BETA1-6 : angle 1.23557 / 0.70 ( 18) link_NAG-ASN : bond 0.00467 / 0.27 ( 63) link_NAG-ASN : angle 2.70309 / 1.93 ( 189) *********************** 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 274 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8215 (p90) cc_final: 0.7997 (p90) REVERT: A 143 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7952 (mtm-85) REVERT: A 184 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7564 (ttp) REVERT: B 571 TRP cc_start: 0.4641 (t-100) cc_final: 0.4199 (t60) REVERT: K 3 GLN cc_start: 0.8527 (mt0) cc_final: 0.8316 (mm-40) REVERT: K 72 ASP cc_start: 0.8184 (t0) cc_final: 0.7590 (t70) REVERT: G 6 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: G 47 MET cc_start: 0.8469 (mmm) cc_final: 0.8140 (mmt) REVERT: G 103 ARG cc_start: 0.8329 (tpp-160) cc_final: 0.8044 (mtp85) REVERT: L 17 ASP cc_start: 0.7380 (t0) cc_final: 0.7077 (m-30) REVERT: L 33 TYR cc_start: 0.7896 (m-80) cc_final: 0.7472 (m-10) REVERT: L 49 ILE cc_start: 0.8712 (mp) cc_final: 0.8097 (tt) REVERT: L 54 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7411 (mtp85) REVERT: H 57 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.7036 (mtpp) REVERT: H 79 TYR cc_start: 0.7880 (m-10) cc_final: 0.7512 (m-80) REVERT: H 82 LEU cc_start: 0.5655 (mp) cc_final: 0.5337 (pp) REVERT: C 207 LYS cc_start: 0.8680 (pttt) cc_final: 0.8273 (tmtt) REVERT: D 624 ASP cc_start: 0.9005 (m-30) cc_final: 0.8374 (m-30) REVERT: D 654 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: M 19 LYS cc_start: 0.8882 (tttt) cc_final: 0.8533 (tttp) REVERT: M 28 THR cc_start: 0.8908 (m) cc_final: 0.8566 (p) REVERT: M 43 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8515 (mmmt) REVERT: M 72 ASP cc_start: 0.7709 (t0) cc_final: 0.7335 (t0) REVERT: M 83 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6470 (mtm-85) REVERT: N 60 ASP cc_start: 0.8099 (p0) cc_final: 0.7005 (t0) REVERT: N 83 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7691 (mm-30) REVERT: N 94 ARG cc_start: 0.5766 (mpt180) cc_final: 0.4795 (tpt170) REVERT: I 13 GLN cc_start: 0.9096 (pm20) cc_final: 0.8887 (pm20) REVERT: J 27 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: J 31 ASN cc_start: 0.8857 (m-40) cc_final: 0.8492 (m110) REVERT: J 94 ARG cc_start: 0.6165 (mpt180) cc_final: 0.4624 (mtp85) outliers start: 38 outliers final: 22 residues processed: 260 average time/residue: 0.1563 time to fit residues: 60.9025 Evaluate side-chains 241 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 143 ARG 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 6 GLN Chi-restraints excluded: chain G residue 81 ASP 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 57 LYS 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 265 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 83 ARG 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 136 optimal weight: 0.0000 chunk 10 optimal weight: 0.2980 chunk 223 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 245 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 205 optimal weight: 0.1980 chunk 16 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 187 optimal weight: 0.5980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3503 r_free = 0.3503 target = 0.091583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.067756 restraints weight = 51301.492| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.38 r_work: 0.2915 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 21751 Z= 0.100 Angle : 0.561 20.506 29691 Z= 0.271 Chirality : 0.047 1.059 3549 Planarity : 0.003 0.033 3610 Dihedral : 4.174 22.571 2747 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 1.50 % Allowed : 8.73 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.17), residues: 2497 helix: 2.30 (0.28), residues: 384 sheet: 1.03 (0.19), residues: 760 loop : -0.44 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 40 TYR 0.015 0.001 TYR M 27 PHE 0.024 0.001 PHE C 53 TRP 0.041 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (21616) covalent geometry : angle 0.51388 / 0.26 (29323) SS BOND : bond 0.00275 / 0.17 ( 37) SS BOND : angle 0.68288 / 0.39 ( 74) hydrogen bonds : bond 0.03341 / 2.18 ( 590) hydrogen bonds : angle 4.04252 / 2.78 ( 1521) link_ALPHA1-3 : bond 0.00475 / 0.25 ( 6) link_ALPHA1-3 : angle 1.83936 / 1.41 ( 18) link_ALPHA1-6 : bond 0.00300 / 0.14 ( 2) link_ALPHA1-6 : angle 1.42648 / 1.01 ( 6) link_BETA1-4 : bond 0.00460 / 0.26 ( 21) link_BETA1-4 : angle 1.50889 / 1.03 ( 63) link_BETA1-6 : bond 0.00388 / 0.19 ( 6) link_BETA1-6 : angle 1.17104 / 0.66 ( 18) link_NAG-ASN : bond 0.00879 / 0.40 ( 63) link_NAG-ASN : angle 2.65037 / 1.81 ( 189) *********************** 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 284 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 0.814 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: 0.8085 (p90) cc_final: 0.7839 (p90) REVERT: A 184 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7659 (ttp) REVERT: K 72 ASP cc_start: 0.8152 (t0) cc_final: 0.7560 (t70) REVERT: G 6 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7212 (pt0) REVERT: G 47 MET cc_start: 0.8406 (mmm) cc_final: 0.8092 (mmt) REVERT: G 103 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.8029 (mtp85) REVERT: L 17 ASP cc_start: 0.7314 (t0) cc_final: 0.7046 (m-30) REVERT: L 33 TYR cc_start: 0.7785 (m-80) cc_final: 0.7360 (m-10) REVERT: L 49 ILE cc_start: 0.8805 (mp) cc_final: 0.8276 (tt) REVERT: L 54 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7397 (mtp85) REVERT: H 3 GLN cc_start: 0.7288 (pm20) cc_final: 0.6994 (pm20) REVERT: H 79 TYR cc_start: 0.7955 (m-10) cc_final: 0.7569 (m-80) REVERT: C 207 LYS cc_start: 0.8687 (pttt) cc_final: 0.8245 (tmtt) REVERT: D 654 GLU cc_start: 0.8320 (tt0) cc_final: 0.7971 (mt-10) REVERT: M 28 THR cc_start: 0.8888 (m) cc_final: 0.8536 (p) REVERT: M 43 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8440 (mmmt) REVERT: M 72 ASP cc_start: 0.7591 (t0) cc_final: 0.7111 (t70) REVERT: M 83 ARG cc_start: 0.6806 (tpp80) cc_final: 0.6322 (mtm-85) REVERT: M 105 GLN cc_start: 0.8554 (mp10) cc_final: 0.8343 (mp10) REVERT: N 60 ASP cc_start: 0.8097 (p0) cc_final: 0.7050 (t0) REVERT: N 83 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7686 (mm-30) REVERT: N 94 ARG cc_start: 0.5655 (mpt180) cc_final: 0.4926 (tpt170) REVERT: E 430 ILE cc_start: 0.8964 (mp) cc_final: 0.8686 (mp) REVERT: I 3 GLN cc_start: 0.8408 (mt0) cc_final: 0.7996 (mm-40) REVERT: I 82 MET cc_start: 0.7976 (mtm) cc_final: 0.7571 (mtm) REVERT: I 105 GLN cc_start: 0.8749 (pm20) cc_final: 0.8520 (pm20) REVERT: J 31 ASN cc_start: 0.8836 (m-40) cc_final: 0.8475 (m110) REVERT: J 79 GLN cc_start: 0.6984 (mp10) cc_final: 0.6623 (mp10) REVERT: J 94 ARG cc_start: 0.6087 (mpt180) cc_final: 0.4592 (mtp85) outliers start: 33 outliers final: 18 residues processed: 269 average time/residue: 0.1580 time to fit residues: 64.0384 Evaluate side-chains 236 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 G residue 6 GLN 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 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 662 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 27 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 238 optimal weight: 0.9980 chunk 221 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 226 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3477 r_free = 0.3477 target = 0.090191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.066113 restraints weight = 51803.364| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.39 r_work: 0.2884 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21751 Z= 0.153 Angle : 0.588 15.076 29691 Z= 0.288 Chirality : 0.045 0.453 3549 Planarity : 0.004 0.052 3610 Dihedral : 4.256 22.377 2745 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer: Outliers : 1.64 % Allowed : 9.05 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.17), residues: 2497 helix: 2.26 (0.28), residues: 384 sheet: 0.95 (0.19), residues: 764 loop : -0.47 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 40 TYR 0.021 0.001 TYR N 91 PHE 0.024 0.001 PHE C 53 TRP 0.025 0.001 TRP H 47 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (21616) covalent geometry : angle 0.55186 / 0.28 (29323) SS BOND : bond 0.00363 / 0.22 ( 37) SS BOND : angle 0.86265 / 0.51 ( 74) hydrogen bonds : bond 0.03803 / 2.48 ( 590) hydrogen bonds : angle 4.09237 / 2.82 ( 1521) link_ALPHA1-3 : bond 0.00426 / 0.22 ( 6) link_ALPHA1-3 : angle 1.90105 / 1.42 ( 18) link_ALPHA1-6 : bond 0.00218 / 0.11 ( 2) link_ALPHA1-6 : angle 1.48739 / 1.04 ( 6) link_BETA1-4 : bond 0.00426 / 0.23 ( 21) link_BETA1-4 : angle 1.61985 / 1.10 ( 63) link_BETA1-6 : bond 0.00321 / 0.16 ( 6) link_BETA1-6 : angle 1.31336 / 0.73 ( 18) link_NAG-ASN : bond 0.00403 / 0.28 ( 63) link_NAG-ASN : angle 2.29028 / 1.60 ( 189) *********************** 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 257 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8218 (p90) cc_final: 0.7994 (p90) REVERT: A 184 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7736 (ttp) REVERT: K 72 ASP cc_start: 0.8256 (t0) cc_final: 0.7645 (t70) REVERT: G 6 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: G 47 MET cc_start: 0.8432 (mmm) cc_final: 0.8113 (mmt) REVERT: G 103 ARG cc_start: 0.8286 (tpp-160) cc_final: 0.8041 (mtp85) REVERT: L 17 ASP cc_start: 0.7435 (t0) cc_final: 0.7141 (m-30) REVERT: L 33 TYR cc_start: 0.7791 (m-80) cc_final: 0.7365 (m-10) REVERT: L 36 TRP cc_start: 0.7876 (m100) cc_final: 0.7618 (m100) REVERT: L 49 ILE cc_start: 0.8812 (mp) cc_final: 0.8341 (tt) REVERT: L 54 ARG cc_start: 0.7651 (mtp85) cc_final: 0.7345 (mtp85) REVERT: L 62 ARG cc_start: 0.4799 (OUTLIER) cc_final: 0.4093 (tmm160) REVERT: L 90 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7894 (ttm-80) REVERT: H 46 GLU cc_start: 0.8099 (tt0) cc_final: 0.7801 (mp0) REVERT: H 79 TYR cc_start: 0.7890 (m-10) cc_final: 0.7527 (m-80) REVERT: C 207 LYS cc_start: 0.8657 (pttt) cc_final: 0.8244 (tmtt) REVERT: M 28 THR cc_start: 0.8953 (m) cc_final: 0.8616 (p) REVERT: M 43 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8483 (mmmt) REVERT: M 72 ASP cc_start: 0.7695 (t0) cc_final: 0.7310 (t0) REVERT: M 83 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6387 (mtm-85) REVERT: N 60 ASP cc_start: 0.8041 (p0) cc_final: 0.7019 (t0) REVERT: N 83 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7692 (mm-30) REVERT: N 94 ARG cc_start: 0.5786 (mpt180) cc_final: 0.4838 (tpt170) REVERT: E 430 ILE cc_start: 0.8988 (mp) cc_final: 0.8715 (mm) REVERT: I 3 GLN cc_start: 0.8527 (mt0) cc_final: 0.8214 (mm-40) REVERT: I 82 MET cc_start: 0.8111 (mtm) cc_final: 0.7618 (mtm) REVERT: J 27 ASP cc_start: 0.7898 (m-30) cc_final: 0.7515 (m-30) REVERT: J 31 ASN cc_start: 0.8870 (m-40) cc_final: 0.8499 (m110) REVERT: J 94 ARG cc_start: 0.6251 (mpt180) cc_final: 0.4678 (mtp85) outliers start: 36 outliers final: 22 residues processed: 242 average time/residue: 0.1657 time to fit residues: 60.6958 Evaluate side-chains 237 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 6 GLN Chi-restraints excluded: chain G residue 81 ASP 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 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL 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 J residue 27 SER 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 74 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 129 optimal weight: 0.0980 chunk 201 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 217 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN ** 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 = 0.3473 r_free = 0.3473 target = 0.089987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065832 restraints weight = 51752.785| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.40 r_work: 0.2874 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 21751 Z= 0.159 Angle : 0.644 25.073 29691 Z= 0.316 Chirality : 0.048 0.671 3549 Planarity : 0.004 0.089 3610 Dihedral : 4.262 23.688 2745 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.80 % Favored : 96.08 % Rotamer: Outliers : 1.59 % Allowed : 9.14 % Favored : 89.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2497 helix: 2.21 (0.28), residues: 384 sheet: 0.88 (0.19), residues: 773 loop : -0.50 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 143 TYR 0.016 0.001 TYR M 27 PHE 0.023 0.001 PHE C 53 TRP 0.022 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (21616) covalent geometry : angle 0.59248 / 0.30 (29323) SS BOND : bond 0.00412 / 0.24 ( 37) SS BOND : angle 0.89305 / 0.52 ( 74) hydrogen bonds : bond 0.03777 / 2.45 ( 590) hydrogen bonds : angle 4.14794 / 2.88 ( 1521) link_ALPHA1-3 : bond 0.00410 / 0.21 ( 6) link_ALPHA1-3 : angle 1.90831 / 1.44 ( 18) link_ALPHA1-6 : bond 0.00206 / 0.10 ( 2) link_ALPHA1-6 : angle 1.49974 / 1.04 ( 6) link_BETA1-4 : bond 0.00396 / 0.23 ( 21) link_BETA1-4 : angle 1.59239 / 1.08 ( 63) link_BETA1-6 : bond 0.00330 / 0.18 ( 6) link_BETA1-6 : angle 1.52189 / 0.84 ( 18) link_NAG-ASN : bond 0.00467 / 0.37 ( 63) link_NAG-ASN : angle 2.99820 / 1.94 ( 189) *********************** 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 256 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.768 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 53 PHE cc_start: 0.8243 (p90) cc_final: 0.8036 (p90) REVERT: A 184 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7870 (ttp) REVERT: K 72 ASP cc_start: 0.8315 (t0) cc_final: 0.7722 (t70) REVERT: G 6 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: G 47 MET cc_start: 0.8442 (mmm) cc_final: 0.8036 (mmt) REVERT: G 103 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.8004 (mtp85) REVERT: L 17 ASP cc_start: 0.7373 (t0) cc_final: 0.7085 (m-30) REVERT: L 33 TYR cc_start: 0.7798 (m-80) cc_final: 0.7373 (m-10) REVERT: L 36 TRP cc_start: 0.7852 (m100) cc_final: 0.7639 (m100) REVERT: L 49 ILE cc_start: 0.8814 (mp) cc_final: 0.8360 (tt) REVERT: L 54 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7360 (mtp85) REVERT: L 84 PHE cc_start: 0.6933 (m-80) cc_final: 0.6621 (m-80) REVERT: L 90 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7883 (ttm-80) REVERT: H 3 GLN cc_start: 0.7395 (pm20) cc_final: 0.7086 (pm20) REVERT: H 66 ARG cc_start: 0.7576 (mtm180) cc_final: 0.6875 (ptm160) REVERT: H 79 TYR cc_start: 0.7970 (m-10) cc_final: 0.7708 (m-80) REVERT: C 207 LYS cc_start: 0.8673 (pttt) cc_final: 0.8247 (tmtt) REVERT: M 28 THR cc_start: 0.8966 (m) cc_final: 0.8647 (p) REVERT: M 72 ASP cc_start: 0.7705 (t0) cc_final: 0.7329 (t0) REVERT: M 83 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6527 (mtm-85) REVERT: N 60 ASP cc_start: 0.8066 (p0) cc_final: 0.7065 (t0) REVERT: N 83 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7638 (mm-30) REVERT: N 94 ARG cc_start: 0.5898 (mpt180) cc_final: 0.4892 (tpt170) REVERT: E 430 ILE cc_start: 0.8950 (mp) cc_final: 0.8712 (mm) REVERT: E 475 MET cc_start: 0.8514 (tpt) cc_final: 0.8128 (tpp) REVERT: F 533 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8658 (mtp) REVERT: I 3 GLN cc_start: 0.8551 (mt0) cc_final: 0.8244 (mm-40) REVERT: I 19 LYS cc_start: 0.8179 (tttt) cc_final: 0.7922 (ttmt) REVERT: I 105 GLN cc_start: 0.8807 (pm20) cc_final: 0.8384 (mm-40) REVERT: J 27 ASP cc_start: 0.7987 (m-30) cc_final: 0.7605 (m-30) REVERT: J 31 ASN cc_start: 0.8878 (m-40) cc_final: 0.8507 (m110) REVERT: J 94 ARG cc_start: 0.6308 (mpt180) cc_final: 0.4839 (mtp85) outliers start: 35 outliers final: 22 residues processed: 240 average time/residue: 0.1562 time to fit residues: 57.1454 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 : 0.865 ------------------------------------------------------------------------------- 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 6 GLN Chi-restraints excluded: chain G residue 81 ASP 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 51 MET 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 265 LEU Chi-restraints excluded: chain M residue 83 ARG 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 662 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 27 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 166 optimal weight: 0.9990 chunk 134 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3492 r_free = 0.3492 target = 0.090981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.066960 restraints weight = 51593.310| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.40 r_work: 0.2903 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21751 Z= 0.109 Angle : 0.588 25.061 29691 Z= 0.286 Chirality : 0.045 0.691 3549 Planarity : 0.003 0.038 3610 Dihedral : 4.174 30.218 2745 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.40 % Favored : 96.40 % Rotamer: Outliers : 1.41 % Allowed : 9.50 % Favored : 89.09 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2497 helix: 2.34 (0.28), residues: 384 sheet: 0.93 (0.19), residues: 769 loop : -0.51 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 40 TYR 0.015 0.001 TYR C 173 PHE 0.022 0.001 PHE C 53 TRP 0.017 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (21616) covalent geometry : angle 0.54290 / 0.28 (29323) SS BOND : bond 0.00362 / 0.21 ( 37) SS BOND : angle 0.79115 / 0.46 ( 74) hydrogen bonds : bond 0.03442 / 2.23 ( 590) hydrogen bonds : angle 4.00773 / 2.76 ( 1521) link_ALPHA1-3 : bond 0.00449 / 0.23 ( 6) link_ALPHA1-3 : angle 1.85433 / 1.42 ( 18) link_ALPHA1-6 : bond 0.00243 / 0.12 ( 2) link_ALPHA1-6 : angle 1.46198 / 1.01 ( 6) link_BETA1-4 : bond 0.00440 / 0.25 ( 21) link_BETA1-4 : angle 1.47524 / 1.01 ( 63) link_BETA1-6 : bond 0.00355 / 0.18 ( 6) link_BETA1-6 : angle 1.29695 / 0.73 ( 18) link_NAG-ASN : bond 0.00509 / 0.32 ( 63) link_NAG-ASN : angle 2.66709 / 1.82 ( 189) *********************** 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 255 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.823 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 184 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7550 (ptm) REVERT: K 72 ASP cc_start: 0.8273 (t0) cc_final: 0.7665 (t70) REVERT: G 6 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7454 (pt0) REVERT: G 47 MET cc_start: 0.8424 (mmm) cc_final: 0.8032 (mmt) REVERT: G 103 ARG cc_start: 0.8221 (tpp-160) cc_final: 0.8004 (mtp85) REVERT: L 17 ASP cc_start: 0.7453 (t0) cc_final: 0.7144 (m-30) REVERT: L 33 TYR cc_start: 0.7776 (m-80) cc_final: 0.7365 (m-10) REVERT: L 36 TRP cc_start: 0.7853 (m100) cc_final: 0.7617 (m100) REVERT: L 49 ILE cc_start: 0.8817 (mp) cc_final: 0.8405 (tt) REVERT: L 72 PHE cc_start: 0.7314 (m-10) cc_final: 0.7040 (m-10) REVERT: L 84 PHE cc_start: 0.6904 (m-80) cc_final: 0.6591 (m-80) REVERT: H 3 GLN cc_start: 0.7383 (pm20) cc_final: 0.7048 (pm20) REVERT: H 46 GLU cc_start: 0.8083 (tt0) cc_final: 0.7700 (tt0) REVERT: H 79 TYR cc_start: 0.8021 (m-10) cc_final: 0.7746 (m-10) REVERT: C 207 LYS cc_start: 0.8738 (pttt) cc_final: 0.8310 (tmtt) REVERT: M 72 ASP cc_start: 0.7634 (t0) cc_final: 0.7147 (t70) REVERT: M 83 ARG cc_start: 0.6911 (tpp80) cc_final: 0.6429 (mtm-85) REVERT: N 60 ASP cc_start: 0.8053 (p0) cc_final: 0.7042 (t0) REVERT: N 83 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7807 (mm-30) REVERT: N 94 ARG cc_start: 0.5780 (mpt180) cc_final: 0.4843 (tpt170) REVERT: E 430 ILE cc_start: 0.8967 (mp) cc_final: 0.8716 (mm) REVERT: E 475 MET cc_start: 0.8443 (tpt) cc_final: 0.8158 (tpp) REVERT: F 533 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8612 (mtp) REVERT: I 3 GLN cc_start: 0.8574 (mt0) cc_final: 0.8290 (mm-40) REVERT: I 105 GLN cc_start: 0.8753 (pm20) cc_final: 0.8353 (mm-40) REVERT: J 27 ASP cc_start: 0.7857 (m-30) cc_final: 0.7508 (m-30) REVERT: J 31 ASN cc_start: 0.8846 (m-40) cc_final: 0.8472 (m110) REVERT: J 94 ARG cc_start: 0.6252 (mpt180) cc_final: 0.4681 (mtp85) outliers start: 31 outliers final: 20 residues processed: 241 average time/residue: 0.1487 time to fit residues: 54.8313 Evaluate side-chains 239 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 G residue 6 GLN Chi-restraints excluded: chain G residue 81 ASP 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 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 662 GLU Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 87 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 70 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3463 r_free = 0.3463 target = 0.089323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065507 restraints weight = 51634.342| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.34 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: 0.8604 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21751 Z= 0.206 Angle : 0.643 22.100 29691 Z= 0.314 Chirality : 0.048 0.696 3549 Planarity : 0.004 0.051 3610 Dihedral : 4.366 29.641 2745 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.12 % Favored : 95.67 % Rotamer: Outliers : 1.18 % Allowed : 9.86 % Favored : 88.95 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.17), residues: 2497 helix: 2.17 (0.28), residues: 384 sheet: 0.84 (0.19), residues: 773 loop : -0.56 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 54 TYR 0.017 0.001 TYR M 27 PHE 0.025 0.002 PHE A 53 TRP 0.016 0.001 TRP H 47 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (21616) covalent geometry : angle 0.60259 / 0.31 (29323) SS BOND : bond 0.00423 / 0.26 ( 37) SS BOND : angle 1.02644 / 0.67 ( 74) hydrogen bonds : bond 0.04112 / 2.66 ( 590) hydrogen bonds : angle 4.16295 / 2.89 ( 1521) link_ALPHA1-3 : bond 0.00427 / 0.22 ( 6) link_ALPHA1-3 : angle 1.96528 / 1.49 ( 18) link_ALPHA1-6 : bond 0.00255 / 0.13 ( 2) link_ALPHA1-6 : angle 1.36461 / 0.94 ( 6) link_BETA1-4 : bond 0.00401 / 0.22 ( 21) link_BETA1-4 : angle 1.63906 / 1.12 ( 63) link_BETA1-6 : bond 0.00316 / 0.18 ( 6) link_BETA1-6 : angle 1.44684 / 0.79 ( 18) link_NAG-ASN : bond 0.00604 / 0.35 ( 63) link_NAG-ASN : angle 2.59876 / 1.82 ( 189) ********************** 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 240 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7739 (ptm) REVERT: K 72 ASP cc_start: 0.8366 (t0) cc_final: 0.7752 (t70) REVERT: G 6 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: G 47 MET cc_start: 0.8467 (mmm) cc_final: 0.7997 (mmt) REVERT: G 103 ARG cc_start: 0.8254 (tpp-160) cc_final: 0.7994 (mtp85) REVERT: L 17 ASP cc_start: 0.7361 (t0) cc_final: 0.7045 (m-30) REVERT: L 33 TYR cc_start: 0.7855 (m-80) cc_final: 0.7427 (m-10) REVERT: L 49 ILE cc_start: 0.8820 (mp) cc_final: 0.8396 (tt) REVERT: L 84 PHE cc_start: 0.6866 (m-80) cc_final: 0.6574 (m-80) REVERT: H 3 GLN cc_start: 0.7437 (pm20) cc_final: 0.7093 (pm20) REVERT: H 46 GLU cc_start: 0.8148 (tt0) cc_final: 0.7807 (tt0) REVERT: H 66 ARG cc_start: 0.7587 (mtm180) cc_final: 0.6908 (ptm160) REVERT: H 79 TYR cc_start: 0.8028 (m-10) cc_final: 0.7748 (m-10) REVERT: H 100 ASP cc_start: 0.8692 (t0) cc_final: 0.8474 (t0) REVERT: C 207 LYS cc_start: 0.8670 (pttt) cc_final: 0.8259 (tmtt) REVERT: D 621 GLU cc_start: 0.8688 (tt0) cc_final: 0.8480 (mt-10) REVERT: M 72 ASP cc_start: 0.7722 (t0) cc_final: 0.7330 (t0) REVERT: M 83 ARG cc_start: 0.7019 (tpp80) cc_final: 0.6677 (mtm-85) REVERT: N 60 ASP cc_start: 0.8190 (p0) cc_final: 0.7209 (t0) REVERT: N 83 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7842 (mm-30) REVERT: N 94 ARG cc_start: 0.6041 (mpt180) cc_final: 0.4828 (tpt170) REVERT: E 430 ILE cc_start: 0.9009 (mp) cc_final: 0.8758 (mm) REVERT: E 475 MET cc_start: 0.8532 (tpt) cc_final: 0.8308 (tpp) REVERT: F 533 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8757 (mtp) REVERT: I 3 GLN cc_start: 0.8639 (mt0) cc_final: 0.8362 (mm-40) REVERT: I 105 GLN cc_start: 0.8768 (pm20) cc_final: 0.8458 (mm-40) REVERT: J 27 ASP cc_start: 0.7933 (m-30) cc_final: 0.7604 (m-30) REVERT: J 31 ASN cc_start: 0.8880 (m-40) cc_final: 0.8507 (m110) outliers start: 26 outliers final: 21 residues processed: 232 average time/residue: 0.1482 time to fit residues: 51.8511 Evaluate side-chains 232 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 G residue 6 GLN 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 51 MET 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 265 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 533 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 233 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 3 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 = 0.3454 r_free = 0.3454 target = 0.088759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.064671 restraints weight = 51759.685| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.37 r_work: 0.2848 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21751 Z= 0.193 Angle : 0.626 17.964 29691 Z= 0.308 Chirality : 0.047 0.519 3549 Planarity : 0.004 0.032 3610 Dihedral : 4.441 30.229 2745 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.00 % Favored : 95.79 % Rotamer: Outliers : 1.73 % Allowed : 9.64 % Favored : 88.64 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.17), residues: 2497 helix: 2.12 (0.28), residues: 384 sheet: 0.99 (0.20), residues: 728 loop : -0.74 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 54 TYR 0.017 0.001 TYR C 173 PHE 0.025 0.002 PHE A 53 TRP 0.041 0.001 TRP L 36 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (21616) covalent geometry : angle 0.59424 / 0.30 (29323) SS BOND : bond 0.00423 / 0.25 ( 37) SS BOND : angle 1.01343 / 0.66 ( 74) hydrogen bonds : bond 0.04116 / 2.67 ( 590) hydrogen bonds : angle 4.20471 / 2.92 ( 1521) link_ALPHA1-3 : bond 0.00405 / 0.21 ( 6) link_ALPHA1-3 : angle 1.94874 / 1.50 ( 18) link_ALPHA1-6 : bond 0.00122 / 0.06 ( 2) link_ALPHA1-6 : angle 1.41731 / 0.95 ( 6) link_BETA1-4 : bond 0.00412 / 0.22 ( 21) link_BETA1-4 : angle 1.60818 / 1.10 ( 63) link_BETA1-6 : bond 0.00287 / 0.16 ( 6) link_BETA1-6 : angle 1.41352 / 0.78 ( 18) link_NAG-ASN : bond 0.00359 / 0.25 ( 63) link_NAG-ASN : angle 2.20393 / 1.53 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4397.12 seconds wall clock time: 76 minutes 20.99 seconds (4580.99 seconds total)