Starting phenix.real_space_refine on Fri Jul 3 23:18:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t76_25735/07_2026/7t76_25735.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t76_25735/07_2026/7t76_25735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t76_25735/07_2026/7t76_25735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t76_25735/07_2026/7t76_25735.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7t76_25735/07_2026/7t76_25735.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t76_25735/07_2026/7t76_25735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t76_25735/07_2026/7t76_25735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t76_25735/07_2026/7t76_25735.map" } resolution = 4.43 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= 0.003 sd= 0.093 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 106 5.16 5 C 10329 2.51 5 N 2742 2.21 5 O 3410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 16587 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "E" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "F" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 791 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 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: "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: 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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "j" 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.68, per 1000 atoms: 0.22 Number of scatterers: 16587 At special positions: 0 Unit cell: (129.95, 132.25, 161, 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 106 16.00 O 3410 8.00 N 2742 7.00 C 10329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.21 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.07 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.09 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.08 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.15 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.20 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.01 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.13 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=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16501 O5 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16501 O5 NAG E 607 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 6 " " BMA c 3 " - " MAN c 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 7 " " MAN j 4 " - " MAN j 5 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 5 " " BMA c 3 " - " MAN c 5 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 4 " " MAN j 4 " - " MAN j 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 137 " " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 88 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 462 " " NAG E 606 " - " ASN E 88 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 160 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 392 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 156 " " NAG b 1 " - " ASN E 197 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 301 " " NAG e 1 " - " ASN E 332 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN E 392 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 156 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 678.8 milliseconds 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 27 sheets defined 24.5% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.653A pdb=" N ARG A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.773A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.827A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 464 removed outlier: 3.783A pdb=" N THR C 464 " --> pdb=" O THR C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 541 Processing helix chain 'D' and resid 542 through 544 No H-bonds generated for 'chain 'D' and resid 542 through 544' Processing helix chain 'D' and resid 573 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 659 removed outlier: 3.802A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 335 through 351 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.870A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.778A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 650 through 661 removed outlier: 4.375A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 611 through 615 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 650 Processing helix chain 'B' and resid 650 through 658 Processing helix chain 'B' and resid 659 through 663 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100I through 100M Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 496 removed outlier: 5.698A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.187A 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: 4.862A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 5.484A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA8, 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: 6.682A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.618A 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 322 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=AA9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.432A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 removed outlier: 7.527A pdb=" N HIS C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 215 through 218 removed outlier: 5.379A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AB5, 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 298 removed outlier: 7.022A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 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 467 through 470 Processing sheet with id=AB6, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.782A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 496 removed outlier: 5.485A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.609A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AC3, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.856A pdb=" N ARG E 169 " --> pdb=" O TYS H 100H" (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG H 100B" --> pdb=" O TYS H 100E" (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 201 through 202 Processing sheet with id=AC5, 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: 6.821A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.683A 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 323 current: chain 'E' and resid 381 through 385 removed outlier: 4.353A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 413 through 421 current: chain 'E' and resid 466 through 470 Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100O through 103 460 hydrogen bonds defined for protein. 1200 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: 2.22 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4817 1.34 - 1.49: 5235 1.49 - 1.64: 6711 1.64 - 1.79: 54 1.79 - 1.94: 88 Bond restraints: 16905 Sorted by residual: bond pdb=" NE1 TRP B 610 " pdb=" CE2 TRP B 610 " ideal model delta sigma weight residual 1.370 1.290 0.080 1.10e-02 8.26e+03 5.33e+01 bond pdb=" CB LEU D 663 " pdb=" CG LEU D 663 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" CA CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sigma weight residual 1.522 1.564 -0.041 7.00e-03 2.04e+04 3.47e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.644 -0.114 2.00e-02 2.50e+03 3.25e+01 ... (remaining 16900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.78: 22907 7.78 - 15.55: 44 15.55 - 23.33: 0 23.33 - 31.11: 0 31.11 - 38.88: 11 Bond angle restraints: 22962 Sorted by residual: angle pdb=" C2 NAG E 604 " pdb=" N2 NAG E 604 " pdb=" C7 NAG E 604 " ideal model delta sigma weight residual 124.56 163.44 -38.88 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 163.08 -38.52 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C2 NAG D 703 " pdb=" N2 NAG D 703 " pdb=" C7 NAG D 703 " ideal model delta sigma weight residual 124.56 162.44 -37.88 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG D 701 " pdb=" N2 NAG D 701 " pdb=" C7 NAG D 701 " ideal model delta sigma weight residual 124.56 161.76 -37.20 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C2 NAG D 702 " pdb=" N2 NAG D 702 " pdb=" C7 NAG D 702 " ideal model delta sigma weight residual 124.56 161.29 -36.73 3.00e+00 1.11e-01 1.50e+02 ... (remaining 22957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8947 17.95 - 35.90: 266 35.90 - 53.85: 67 53.85 - 71.80: 29 71.80 - 89.75: 17 Dihedral angle restraints: 9326 sinusoidal: 3748 harmonic: 5578 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual -86.00 -171.83 85.83 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -169.76 83.76 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS D 598 " pdb=" SG CYS D 598 " pdb=" SG CYS D 604 " pdb=" CB CYS D 604 " ideal model delta sinusoidal sigma weight residual 93.00 153.96 -60.96 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 9323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2110 0.132 - 0.263: 499 0.263 - 0.395: 203 0.395 - 0.527: 66 0.527 - 0.659: 1 Chirality restraints: 2879 Sorted by residual: chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.99e+02 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.93e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.85e+02 ... (remaining 2876 not shown) Planarity restraints: 2843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " -0.373 2.00e-02 2.50e+03 3.18e-01 1.27e+03 pdb=" C7 NAG Z 1 " 0.092 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " 0.557 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG S 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " 0.073 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " -0.537 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.355 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG S 2 " 0.090 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " -0.109 2.00e-02 2.50e+03 ... (remaining 2840 not shown) Histogram of nonbonded interaction distances: 0.53 - 1.40: 13 1.40 - 2.28: 43 2.28 - 3.15: 13738 3.15 - 4.03: 43120 4.03 - 4.90: 75419 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132333 Sorted by model distance: nonbonded pdb=" C ASN E 234 " pdb=" C2 NAG E 607 " model vdw 0.530 2.960 nonbonded pdb=" CA ASN E 234 " pdb=" C3 NAG E 607 " model vdw 0.700 3.900 nonbonded pdb=" O ASN E 234 " pdb=" N2 NAG E 607 " model vdw 0.816 3.120 nonbonded pdb=" CB PHE E 233 " pdb=" O6 NAG E 607 " model vdw 0.928 3.440 nonbonded pdb=" CA ASN E 234 " pdb=" O3 NAG E 607 " model vdw 0.962 3.470 ... (remaining 132328 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' and resid 32 through 605) selection = (chain 'E' and resid 32 through 605) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'S' selection = chain 'c' selection = chain 'i' } ncs_group { reference = (chain 'Z' and (resid 1 or resid 4 through 6)) selection = (chain 'j' and (resid 2 or resid 5 through 7)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.850 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.024 0.985 17044 Z= 1.536 Angle : 2.010 38.881 23339 Z= 1.180 Chirality : 0.143 0.659 2879 Planarity : 0.017 0.318 2788 Dihedral : 10.617 89.752 5630 Min Nonbonded Distance : 0.530 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.38 % Favored : 96.36 % Rotamer: Outliers : 0.77 % Allowed : 1.00 % Favored : 98.23 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.19), residues: 1894 helix: -0.17 (0.24), residues: 378 sheet: 0.62 (0.22), residues: 508 loop : 0.28 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 192 TYR 0.058 0.008 TYR C 40 PHE 0.032 0.006 PHE E 233 TRP 0.050 0.010 TRP E 96 HIS 0.017 0.003 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.02162 / 1.15 (16905) covalent geometry : angle 1.96917 / 1.18 (22962) SS BOND : bond 0.05257 / 3.61 ( 34) SS BOND : angle 3.45474 / 2.43 ( 68) hydrogen bonds : bond 0.17061 / 11.45 ( 460) hydrogen bonds : angle 7.63151 / 5.49 ( 1200) Misc. bond : bond 0.90660 / 45.91 ( 2) link_ALPHA1-3 : bond 0.00409 / 0.22 ( 7) link_ALPHA1-3 : angle 2.62497 / 1.65 ( 21) link_ALPHA1-6 : bond 0.00309 / 0.15 ( 7) link_ALPHA1-6 : angle 1.42300 / 0.91 ( 21) link_BETA1-4 : bond 0.06022 / 3.96 ( 34) link_BETA1-4 : angle 5.02996 / 3.36 ( 102) link_NAG-ASN : bond 0.07423 / 4.69 ( 55) link_NAG-ASN : angle 3.16228 / 2.23 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 436 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ILE cc_start: 0.9408 (pt) cc_final: 0.9197 (mp) REVERT: A 254 VAL cc_start: 0.9515 (t) cc_final: 0.9127 (p) REVERT: A 374 HIS cc_start: 0.7329 (t-170) cc_final: 0.6930 (t-90) REVERT: C 53 PHE cc_start: 0.7584 (m-80) cc_final: 0.6988 (m-10) REVERT: C 69 TRP cc_start: 0.8404 (m-90) cc_final: 0.7710 (m-10) REVERT: C 122 LEU cc_start: 0.9362 (mt) cc_final: 0.9132 (mp) REVERT: C 136 ASN cc_start: 0.6442 (t0) cc_final: 0.6057 (m110) REVERT: D 610 TRP cc_start: 0.6222 (p90) cc_final: 0.5979 (p-90) REVERT: D 655 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8532 (mmmm) REVERT: E 42 VAL cc_start: 0.9298 (t) cc_final: 0.9016 (p) REVERT: E 165 LEU cc_start: 0.9258 (mt) cc_final: 0.8939 (mp) REVERT: E 180 ASP cc_start: 0.8583 (m-30) cc_final: 0.8383 (m-30) REVERT: E 186 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8243 (ptm160) REVERT: E 373 THR cc_start: 0.9127 (p) cc_final: 0.8926 (p) REVERT: E 450 THR cc_start: 0.9263 (p) cc_final: 0.9044 (p) REVERT: F 538 THR cc_start: 0.8610 (p) cc_final: 0.8349 (p) REVERT: F 606 THR cc_start: 0.8958 (p) cc_final: 0.8589 (t) REVERT: F 607 ASN cc_start: 0.8474 (m-40) cc_final: 0.8108 (p0) REVERT: F 624 ASP cc_start: 0.8399 (m-30) cc_final: 0.7959 (t0) REVERT: F 652 GLN cc_start: 0.7896 (tp40) cc_final: 0.7637 (tp40) REVERT: B 543 ASN cc_start: 0.8074 (m-40) cc_final: 0.7809 (t0) REVERT: B 584 GLU cc_start: 0.8922 (tt0) cc_final: 0.8233 (tp30) REVERT: B 643 TYR cc_start: 0.8935 (m-10) cc_final: 0.8225 (m-10) REVERT: L 34 SER cc_start: 0.8990 (m) cc_final: 0.8770 (p) REVERT: L 39 HIS cc_start: 0.8878 (t-90) cc_final: 0.8577 (m-70) REVERT: L 50 GLU cc_start: 0.8511 (tt0) cc_final: 0.8055 (tm-30) REVERT: L 53 ASN cc_start: 0.8897 (m-40) cc_final: 0.8154 (m-40) REVERT: L 75 ILE cc_start: 0.8474 (mt) cc_final: 0.8271 (mt) REVERT: L 91 TYR cc_start: 0.7852 (t80) cc_final: 0.7550 (t80) REVERT: L 98 PHE cc_start: 0.8669 (m-80) cc_final: 0.8434 (m-80) REVERT: H 18 LEU cc_start: 0.8334 (tt) cc_final: 0.7381 (tt) REVERT: H 20 LEU cc_start: 0.9317 (mt) cc_final: 0.9060 (mt) REVERT: H 29 PHE cc_start: 0.8789 (t80) cc_final: 0.8179 (t80) REVERT: H 43 LYS cc_start: 0.8998 (mptt) cc_final: 0.8452 (pttp) REVERT: H 53 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7670 (p0) REVERT: H 68 THR cc_start: 0.9158 (m) cc_final: 0.8740 (t) outliers start: 13 outliers final: 2 residues processed: 448 average time/residue: 0.1338 time to fit residues: 89.3071 Evaluate side-chains 227 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 223 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS C 167 ASN C 190 HIS C 363 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN E 374 HIS F 591 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.069610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.053393 restraints weight = 68312.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.055425 restraints weight = 39200.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.056847 restraints weight = 26992.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.057843 restraints weight = 20945.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.058528 restraints weight = 17508.445| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17044 Z= 0.177 Angle : 0.895 21.430 23339 Z= 0.419 Chirality : 0.053 0.709 2879 Planarity : 0.004 0.047 2788 Dihedral : 5.514 25.898 2073 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.52 % Rotamer: Outliers : 0.06 % Allowed : 2.30 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.19), residues: 1894 helix: 0.08 (0.25), residues: 423 sheet: 0.39 (0.22), residues: 528 loop : -0.17 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 273 TYR 0.017 0.002 TYR E 435 PHE 0.041 0.002 PHE E 233 TRP 0.027 0.002 TRP C 96 HIS 0.007 0.001 HIS E 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (16905) covalent geometry : angle 0.79893 / 0.40 (22962) SS BOND : bond 0.00393 / 0.22 ( 34) SS BOND : angle 1.37893 / 0.95 ( 68) hydrogen bonds : bond 0.06067 / 4.17 ( 460) hydrogen bonds : angle 6.05222 / 4.38 ( 1200) Misc. bond : bond 0.00109 / 0.05 ( 2) link_ALPHA1-3 : bond 0.00524 / 0.28 ( 7) link_ALPHA1-3 : angle 2.04463 / 1.35 ( 21) link_ALPHA1-6 : bond 0.00581 / 0.28 ( 7) link_ALPHA1-6 : angle 1.47768 / 0.94 ( 21) link_BETA1-4 : bond 0.00892 / 0.65 ( 34) link_BETA1-4 : angle 3.24572 / 2.14 ( 102) link_NAG-ASN : bond 0.00583 / 0.33 ( 55) link_NAG-ASN : angle 4.03453 / 3.04 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7049 (m-10) cc_final: 0.6573 (m-10) REVERT: A 98 ASN cc_start: 0.8540 (t0) cc_final: 0.7576 (m-40) REVERT: A 181 ILE cc_start: 0.9471 (pt) cc_final: 0.9000 (mm) REVERT: A 374 HIS cc_start: 0.7772 (t-170) cc_final: 0.7506 (t-90) REVERT: C 53 PHE cc_start: 0.7907 (m-80) cc_final: 0.7502 (m-10) REVERT: C 69 TRP cc_start: 0.8581 (m-90) cc_final: 0.8109 (m-10) REVERT: C 111 LEU cc_start: 0.9474 (mm) cc_final: 0.9061 (mt) REVERT: C 136 ASN cc_start: 0.6412 (t0) cc_final: 0.6153 (m110) REVERT: C 210 PHE cc_start: 0.8687 (m-80) cc_final: 0.8421 (m-10) REVERT: C 260 LEU cc_start: 0.9262 (mt) cc_final: 0.9023 (mt) REVERT: C 416 LEU cc_start: 0.8875 (mt) cc_final: 0.8454 (pp) REVERT: D 546 SER cc_start: 0.7149 (t) cc_final: 0.6943 (t) REVERT: D 584 GLU cc_start: 0.9039 (tp30) cc_final: 0.8205 (tm-30) REVERT: D 607 ASN cc_start: 0.8423 (m110) cc_final: 0.8071 (p0) REVERT: D 657 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8585 (mp0) REVERT: E 180 ASP cc_start: 0.8708 (m-30) cc_final: 0.8347 (m-30) REVERT: E 315 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8834 (mp10) REVERT: F 574 LYS cc_start: 0.6585 (pttm) cc_final: 0.6042 (mmpt) REVERT: F 607 ASN cc_start: 0.8407 (m-40) cc_final: 0.7973 (p0) REVERT: F 630 GLN cc_start: 0.9157 (mt0) cc_final: 0.8914 (mp10) REVERT: F 647 GLU cc_start: 0.8369 (pt0) cc_final: 0.7815 (pt0) REVERT: F 655 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8828 (mmmt) REVERT: B 530 MET cc_start: 0.8212 (mtp) cc_final: 0.8006 (ppp) REVERT: B 538 THR cc_start: 0.9079 (t) cc_final: 0.8854 (t) REVERT: B 584 GLU cc_start: 0.8620 (tt0) cc_final: 0.8155 (tp30) REVERT: B 632 ASP cc_start: 0.9141 (t0) cc_final: 0.8829 (p0) REVERT: B 643 TYR cc_start: 0.8638 (m-10) cc_final: 0.7993 (m-10) REVERT: L 91 TYR cc_start: 0.8061 (t80) cc_final: 0.7580 (t80) REVERT: L 104 LEU cc_start: 0.7697 (tt) cc_final: 0.6586 (tp) REVERT: H 18 LEU cc_start: 0.8474 (tt) cc_final: 0.8194 (tt) REVERT: H 68 THR cc_start: 0.8764 (m) cc_final: 0.8487 (t) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.1250 time to fit residues: 58.7659 Evaluate side-chains 195 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 73 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN C 190 HIS ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS F 652 GLN B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.067341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.050868 restraints weight = 71091.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.052782 restraints weight = 41538.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.054127 restraints weight = 29049.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.055069 restraints weight = 22757.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.055689 restraints weight = 19202.862| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 17044 Z= 0.197 Angle : 0.788 19.145 23339 Z= 0.375 Chirality : 0.048 0.466 2879 Planarity : 0.005 0.176 2788 Dihedral : 5.312 28.977 2073 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.19), residues: 1894 helix: 0.34 (0.27), residues: 390 sheet: 0.15 (0.21), residues: 545 loop : -0.28 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 19 TYR 0.021 0.002 TYR E 484 PHE 0.025 0.002 PHE E 176 TRP 0.019 0.002 TRP E 69 HIS 0.008 0.001 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (16905) covalent geometry : angle 0.71695 / 0.36 (22962) SS BOND : bond 0.00495 / 0.30 ( 34) SS BOND : angle 1.09532 / 0.73 ( 68) hydrogen bonds : bond 0.04704 / 3.22 ( 460) hydrogen bonds : angle 5.66221 / 4.11 ( 1200) Misc. bond : bond 0.00809 / 0.42 ( 2) link_ALPHA1-3 : bond 0.00499 / 0.25 ( 7) link_ALPHA1-3 : angle 1.95068 / 1.28 ( 21) link_ALPHA1-6 : bond 0.00459 / 0.23 ( 7) link_ALPHA1-6 : angle 1.51525 / 0.96 ( 21) link_BETA1-4 : bond 0.00641 / 0.48 ( 34) link_BETA1-4 : angle 2.59724 / 1.73 ( 102) link_NAG-ASN : bond 0.00529 / 0.35 ( 55) link_NAG-ASN : angle 3.28770 / 2.45 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9301 (ttt) cc_final: 0.9100 (ttm) REVERT: A 180 ASP cc_start: 0.8483 (m-30) cc_final: 0.7942 (p0) REVERT: A 286 VAL cc_start: 0.9437 (t) cc_final: 0.9015 (p) REVERT: A 374 HIS cc_start: 0.7859 (t-170) cc_final: 0.7635 (t-90) REVERT: C 69 TRP cc_start: 0.8682 (m-90) cc_final: 0.8068 (m-10) REVERT: C 111 LEU cc_start: 0.9471 (mm) cc_final: 0.9056 (mt) REVERT: C 136 ASN cc_start: 0.6732 (t0) cc_final: 0.6424 (m110) REVERT: C 210 PHE cc_start: 0.8782 (m-80) cc_final: 0.8264 (m-10) REVERT: C 426 MET cc_start: 0.9234 (ttp) cc_final: 0.8937 (ttp) REVERT: C 477 ASP cc_start: 0.8594 (m-30) cc_final: 0.8330 (p0) REVERT: D 584 GLU cc_start: 0.9162 (tp30) cc_final: 0.8187 (tm-30) REVERT: D 607 ASN cc_start: 0.8425 (m110) cc_final: 0.8098 (p0) REVERT: D 648 GLU cc_start: 0.8767 (pp20) cc_final: 0.8080 (pp20) REVERT: D 657 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8492 (mp0) REVERT: E 69 TRP cc_start: 0.9023 (m-10) cc_final: 0.8767 (m-10) REVERT: E 180 ASP cc_start: 0.8806 (m-30) cc_final: 0.8320 (m-30) REVERT: E 315 GLN cc_start: 0.9355 (mm-40) cc_final: 0.8893 (mp10) REVERT: F 574 LYS cc_start: 0.7529 (pttm) cc_final: 0.7159 (mmpt) REVERT: F 576 LEU cc_start: 0.8708 (mt) cc_final: 0.8071 (tt) REVERT: F 606 THR cc_start: 0.8634 (p) cc_final: 0.8276 (t) REVERT: F 607 ASN cc_start: 0.8421 (m-40) cc_final: 0.7816 (p0) REVERT: F 647 GLU cc_start: 0.8532 (pt0) cc_final: 0.8155 (pt0) REVERT: B 540 GLN cc_start: 0.9239 (mm110) cc_final: 0.7980 (mt0) REVERT: B 584 GLU cc_start: 0.8710 (tt0) cc_final: 0.8374 (tp30) REVERT: B 601 LYS cc_start: 0.8991 (mmtm) cc_final: 0.8757 (mmmm) REVERT: B 643 TYR cc_start: 0.8714 (m-10) cc_final: 0.8193 (m-10) REVERT: L 49 TYR cc_start: 0.9001 (p90) cc_final: 0.8278 (p90) REVERT: L 53 ASN cc_start: 0.8677 (m-40) cc_final: 0.7975 (t0) REVERT: L 91 TYR cc_start: 0.7910 (t80) cc_final: 0.7484 (t80) REVERT: L 98 PHE cc_start: 0.7887 (m-80) cc_final: 0.7672 (m-10) REVERT: H 67 PHE cc_start: 0.7338 (m-10) cc_final: 0.7075 (m-10) REVERT: H 68 THR cc_start: 0.8761 (m) cc_final: 0.8297 (p) REVERT: H 80 LEU cc_start: 0.9088 (tp) cc_final: 0.8721 (tp) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1219 time to fit residues: 47.8218 Evaluate side-chains 172 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 102 optimal weight: 0.0970 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 607 ASN D 630 GLN F 591 GLN F 651 ASN F 652 GLN B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 39 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.067009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.050517 restraints weight = 70009.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.052428 restraints weight = 40936.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.053773 restraints weight = 28482.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.054693 restraints weight = 22292.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.055329 restraints weight = 18825.798| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17044 Z= 0.161 Angle : 0.706 19.057 23339 Z= 0.337 Chirality : 0.047 0.441 2879 Planarity : 0.004 0.105 2788 Dihedral : 5.035 27.784 2073 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.19), residues: 1894 helix: 0.31 (0.27), residues: 396 sheet: 0.08 (0.21), residues: 569 loop : -0.37 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 617 TYR 0.017 0.001 TYR E 384 PHE 0.021 0.001 PHE E 176 TRP 0.021 0.002 TRP A 69 HIS 0.006 0.001 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (16905) covalent geometry : angle 0.63665 / 0.32 (22962) SS BOND : bond 0.00318 / 0.19 ( 34) SS BOND : angle 0.98400 / 0.67 ( 68) hydrogen bonds : bond 0.04250 / 2.90 ( 460) hydrogen bonds : angle 5.31422 / 3.83 ( 1200) Misc. bond : bond 0.00375 / 0.20 ( 2) link_ALPHA1-3 : bond 0.00490 / 0.25 ( 7) link_ALPHA1-3 : angle 1.90003 / 1.26 ( 21) link_ALPHA1-6 : bond 0.00471 / 0.24 ( 7) link_ALPHA1-6 : angle 1.46068 / 0.94 ( 21) link_BETA1-4 : bond 0.00626 / 0.48 ( 34) link_BETA1-4 : angle 2.39472 / 1.59 ( 102) link_NAG-ASN : bond 0.00495 / 0.31 ( 55) link_NAG-ASN : angle 3.08042 / 2.33 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8567 (m-30) cc_final: 0.8174 (m-30) REVERT: A 374 HIS cc_start: 0.7883 (t-170) cc_final: 0.7667 (t-90) REVERT: A 494 LEU cc_start: 0.8818 (tt) cc_final: 0.8464 (tt) REVERT: C 69 TRP cc_start: 0.8717 (m-90) cc_final: 0.8037 (m-10) REVERT: C 111 LEU cc_start: 0.9472 (mm) cc_final: 0.9061 (mt) REVERT: C 136 ASN cc_start: 0.6791 (t0) cc_final: 0.6553 (m110) REVERT: C 210 PHE cc_start: 0.8855 (m-80) cc_final: 0.8437 (m-10) REVERT: D 584 GLU cc_start: 0.9172 (tp30) cc_final: 0.8244 (tm-30) REVERT: D 607 ASN cc_start: 0.8266 (m-40) cc_final: 0.7967 (p0) REVERT: D 648 GLU cc_start: 0.8810 (pp20) cc_final: 0.8582 (pp20) REVERT: E 180 ASP cc_start: 0.8800 (m-30) cc_final: 0.8277 (m-30) REVERT: F 576 LEU cc_start: 0.8724 (mt) cc_final: 0.8114 (tt) REVERT: F 647 GLU cc_start: 0.8401 (pt0) cc_final: 0.7985 (pt0) REVERT: F 652 GLN cc_start: 0.8124 (tp40) cc_final: 0.7889 (tp-100) REVERT: B 540 GLN cc_start: 0.9261 (mm110) cc_final: 0.7975 (mt0) REVERT: B 584 GLU cc_start: 0.8802 (tt0) cc_final: 0.8089 (tp30) REVERT: B 591 GLN cc_start: 0.9312 (tp40) cc_final: 0.8842 (tp40) REVERT: B 601 LYS cc_start: 0.8979 (mmtm) cc_final: 0.8748 (mmmm) REVERT: B 643 TYR cc_start: 0.8868 (m-10) cc_final: 0.8421 (m-10) REVERT: L 49 TYR cc_start: 0.8962 (p90) cc_final: 0.8050 (p90) REVERT: L 53 ASN cc_start: 0.8757 (m-40) cc_final: 0.8130 (t0) REVERT: L 91 TYR cc_start: 0.7746 (t80) cc_final: 0.7362 (t80) REVERT: L 98 PHE cc_start: 0.7901 (m-80) cc_final: 0.7659 (m-10) REVERT: H 68 THR cc_start: 0.8964 (m) cc_final: 0.8618 (p) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1074 time to fit residues: 39.3156 Evaluate side-chains 168 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 144 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN C 203 GLN D 630 GLN E 85 HIS E 478 ASN B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.062856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.046739 restraints weight = 72683.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.048463 restraints weight = 43117.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.049655 restraints weight = 30545.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.050544 restraints weight = 24158.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.051041 restraints weight = 20558.568| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 17044 Z= 0.344 Angle : 0.941 18.351 23339 Z= 0.445 Chirality : 0.051 0.437 2879 Planarity : 0.005 0.054 2788 Dihedral : 5.546 34.102 2073 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 1894 helix: 0.30 (0.27), residues: 372 sheet: -0.32 (0.22), residues: 537 loop : -0.64 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 192 TYR 0.020 0.002 TYR E 384 PHE 0.020 0.002 PHE E 210 TRP 0.022 0.003 TRP B 623 HIS 0.009 0.002 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.34 (16905) covalent geometry : angle 0.87176 / 0.43 (22962) SS BOND : bond 0.00547 / 0.31 ( 34) SS BOND : angle 2.27088 / 1.33 ( 68) hydrogen bonds : bond 0.04816 / 3.36 ( 460) hydrogen bonds : angle 5.68499 / 4.08 ( 1200) Misc. bond : bond 0.00254 / 0.13 ( 2) link_ALPHA1-3 : bond 0.00444 / 0.20 ( 7) link_ALPHA1-3 : angle 2.16375 / 1.39 ( 21) link_ALPHA1-6 : bond 0.00340 / 0.18 ( 7) link_ALPHA1-6 : angle 1.63142 / 1.05 ( 21) link_BETA1-4 : bond 0.00618 / 0.44 ( 34) link_BETA1-4 : angle 2.65352 / 1.79 ( 102) link_NAG-ASN : bond 0.00795 / 0.57 ( 55) link_NAG-ASN : angle 3.45837 / 2.61 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9516 (ttt) cc_final: 0.9163 (ttm) REVERT: C 53 PHE cc_start: 0.8553 (m-10) cc_final: 0.8210 (m-80) REVERT: C 111 LEU cc_start: 0.9530 (mm) cc_final: 0.9092 (mt) REVERT: C 207 LYS cc_start: 0.8449 (pttt) cc_final: 0.8212 (tptt) REVERT: C 434 MET cc_start: 0.8741 (mtm) cc_final: 0.8524 (mtp) REVERT: D 584 GLU cc_start: 0.9209 (tp30) cc_final: 0.8338 (tm-30) REVERT: E 180 ASP cc_start: 0.8948 (m-30) cc_final: 0.8369 (m-30) REVERT: F 576 LEU cc_start: 0.8789 (mt) cc_final: 0.8174 (tt) REVERT: F 584 GLU cc_start: 0.8633 (tp30) cc_final: 0.8154 (tm-30) REVERT: F 591 GLN cc_start: 0.9551 (tt0) cc_final: 0.9041 (tt0) REVERT: F 647 GLU cc_start: 0.8476 (pt0) cc_final: 0.8151 (pt0) REVERT: F 652 GLN cc_start: 0.8421 (tp40) cc_final: 0.8110 (tp-100) REVERT: B 589 ASP cc_start: 0.8887 (m-30) cc_final: 0.8595 (p0) REVERT: B 601 LYS cc_start: 0.9168 (mmtm) cc_final: 0.8800 (mmmm) REVERT: L 50 GLU cc_start: 0.8539 (tt0) cc_final: 0.8300 (tt0) REVERT: L 91 TYR cc_start: 0.7807 (t80) cc_final: 0.7480 (t80) REVERT: H 68 THR cc_start: 0.8914 (m) cc_final: 0.8447 (p) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.1142 time to fit residues: 35.1371 Evaluate side-chains 140 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 178 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS D 630 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN L 17 GLN L 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.048588 restraints weight = 70932.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.050423 restraints weight = 41123.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051701 restraints weight = 28697.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.052606 restraints weight = 22588.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.053187 restraints weight = 19152.446| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17044 Z= 0.153 Angle : 0.725 19.043 23339 Z= 0.345 Chirality : 0.047 0.442 2879 Planarity : 0.004 0.054 2788 Dihedral : 5.148 29.327 2073 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Rotamer: Outliers : 0.06 % Allowed : 1.30 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.19), residues: 1894 helix: 0.42 (0.27), residues: 390 sheet: -0.29 (0.22), residues: 553 loop : -0.65 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 192 TYR 0.011 0.001 TYR E 384 PHE 0.017 0.001 PHE C 361 TRP 0.037 0.002 TRP A 69 HIS 0.016 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16905) covalent geometry : angle 0.66131 / 0.33 (22962) SS BOND : bond 0.00452 / 0.31 ( 34) SS BOND : angle 1.35318 / 0.91 ( 68) hydrogen bonds : bond 0.04269 / 2.93 ( 460) hydrogen bonds : angle 5.25225 / 3.76 ( 1200) Misc. bond : bond 0.00342 / 0.18 ( 2) link_ALPHA1-3 : bond 0.00459 / 0.23 ( 7) link_ALPHA1-3 : angle 1.96407 / 1.31 ( 21) link_ALPHA1-6 : bond 0.00452 / 0.23 ( 7) link_ALPHA1-6 : angle 1.46931 / 0.95 ( 21) link_BETA1-4 : bond 0.00614 / 0.47 ( 34) link_BETA1-4 : angle 2.30176 / 1.53 ( 102) link_NAG-ASN : bond 0.00517 / 0.35 ( 55) link_NAG-ASN : angle 2.96416 / 2.34 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8739 (m-30) cc_final: 0.8112 (m-30) REVERT: A 374 HIS cc_start: 0.8227 (t70) cc_final: 0.7646 (t-90) REVERT: C 53 PHE cc_start: 0.8421 (m-10) cc_final: 0.8177 (m-10) REVERT: C 104 MET cc_start: 0.9350 (tmm) cc_final: 0.9139 (tmm) REVERT: C 111 LEU cc_start: 0.9454 (mm) cc_final: 0.9038 (mt) REVERT: C 207 LYS cc_start: 0.8443 (pttt) cc_final: 0.8202 (tptt) REVERT: D 584 GLU cc_start: 0.9238 (tp30) cc_final: 0.8382 (tm-30) REVERT: D 607 ASN cc_start: 0.8065 (m-40) cc_final: 0.7799 (p0) REVERT: E 180 ASP cc_start: 0.8933 (m-30) cc_final: 0.8279 (m-30) REVERT: E 479 TRP cc_start: 0.8707 (m-90) cc_final: 0.8230 (m-90) REVERT: F 530 MET cc_start: 0.8103 (mmm) cc_final: 0.7848 (mmt) REVERT: F 576 LEU cc_start: 0.8631 (mt) cc_final: 0.8071 (tt) REVERT: F 584 GLU cc_start: 0.8437 (tp30) cc_final: 0.7911 (tm-30) REVERT: F 591 GLN cc_start: 0.9459 (tt0) cc_final: 0.8773 (tt0) REVERT: F 601 LYS cc_start: 0.8887 (tptt) cc_final: 0.8317 (tppp) REVERT: F 647 GLU cc_start: 0.8382 (pt0) cc_final: 0.8011 (pt0) REVERT: B 601 LYS cc_start: 0.9091 (mmtm) cc_final: 0.8851 (mmmm) REVERT: B 607 ASN cc_start: 0.8212 (m-40) cc_final: 0.7974 (m-40) REVERT: L 50 GLU cc_start: 0.8446 (tt0) cc_final: 0.8212 (tt0) REVERT: L 91 TYR cc_start: 0.7644 (t80) cc_final: 0.7301 (t80) REVERT: L 98 PHE cc_start: 0.8099 (m-10) cc_final: 0.7842 (m-10) REVERT: H 68 THR cc_start: 0.8921 (m) cc_final: 0.8497 (p) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1242 time to fit residues: 40.6542 Evaluate side-chains 162 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 76 optimal weight: 0.0370 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 630 GLN E 85 HIS E 246 GLN L 17 GLN L 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.066570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.050327 restraints weight = 70158.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.052239 restraints weight = 40291.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.053567 restraints weight = 27829.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.054497 restraints weight = 21629.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055154 restraints weight = 18192.725| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17044 Z= 0.117 Angle : 0.670 18.782 23339 Z= 0.317 Chirality : 0.046 0.423 2879 Planarity : 0.004 0.055 2788 Dihedral : 4.846 26.766 2073 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.83 % Rotamer: Outliers : 0.12 % Allowed : 0.94 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.20), residues: 1894 helix: 0.51 (0.27), residues: 405 sheet: -0.09 (0.22), residues: 536 loop : -0.56 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 617 TYR 0.011 0.001 TYR E 484 PHE 0.015 0.001 PHE E 176 TRP 0.041 0.002 TRP A 69 HIS 0.010 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (16905) covalent geometry : angle 0.60392 / 0.30 (22962) SS BOND : bond 0.00311 / 0.21 ( 34) SS BOND : angle 1.19795 / 0.74 ( 68) hydrogen bonds : bond 0.03860 / 2.64 ( 460) hydrogen bonds : angle 5.04173 / 3.61 ( 1200) Misc. bond : bond 0.00330 / 0.17 ( 2) link_ALPHA1-3 : bond 0.00521 / 0.27 ( 7) link_ALPHA1-3 : angle 1.82786 / 1.22 ( 21) link_ALPHA1-6 : bond 0.00475 / 0.24 ( 7) link_ALPHA1-6 : angle 1.42306 / 0.91 ( 21) link_BETA1-4 : bond 0.00652 / 0.49 ( 34) link_BETA1-4 : angle 2.17673 / 1.44 ( 102) link_NAG-ASN : bond 0.00496 / 0.32 ( 55) link_NAG-ASN : angle 2.93255 / 2.37 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8686 (m-30) cc_final: 0.8030 (m-30) REVERT: A 374 HIS cc_start: 0.8172 (t70) cc_final: 0.7236 (t-90) REVERT: C 104 MET cc_start: 0.9296 (tmm) cc_final: 0.9009 (tmm) REVERT: C 111 LEU cc_start: 0.9412 (mm) cc_final: 0.9058 (mt) REVERT: C 207 LYS cc_start: 0.8462 (pttt) cc_final: 0.8223 (tptt) REVERT: C 210 PHE cc_start: 0.8936 (m-80) cc_final: 0.8561 (m-10) REVERT: D 584 GLU cc_start: 0.9190 (tp30) cc_final: 0.8333 (tm-30) REVERT: E 92 GLU cc_start: 0.8737 (tt0) cc_final: 0.8431 (tt0) REVERT: E 95 MET cc_start: 0.8540 (mmp) cc_final: 0.8224 (mmm) REVERT: E 180 ASP cc_start: 0.8910 (m-30) cc_final: 0.8287 (m-30) REVERT: E 479 TRP cc_start: 0.8511 (m-90) cc_final: 0.8198 (m-90) REVERT: F 576 LEU cc_start: 0.8622 (mt) cc_final: 0.8053 (tt) REVERT: F 584 GLU cc_start: 0.8469 (tp30) cc_final: 0.7834 (tm-30) REVERT: F 601 LYS cc_start: 0.8821 (tptt) cc_final: 0.8257 (tppp) REVERT: F 630 GLN cc_start: 0.9212 (mt0) cc_final: 0.8940 (mt0) REVERT: F 647 GLU cc_start: 0.8315 (pt0) cc_final: 0.7951 (pt0) REVERT: F 655 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8511 (mmmt) REVERT: B 591 GLN cc_start: 0.9282 (tp40) cc_final: 0.8803 (tp40) REVERT: B 633 LYS cc_start: 0.9492 (mtpt) cc_final: 0.9238 (mtmt) REVERT: L 49 TYR cc_start: 0.8994 (p90) cc_final: 0.8053 (p90) REVERT: L 53 ASN cc_start: 0.8687 (m-40) cc_final: 0.8143 (t0) REVERT: L 91 TYR cc_start: 0.7637 (t80) cc_final: 0.7329 (t80) REVERT: H 19 ARG cc_start: 0.8957 (tpt90) cc_final: 0.7740 (mmm160) REVERT: H 68 THR cc_start: 0.8859 (m) cc_final: 0.8422 (p) outliers start: 2 outliers final: 0 residues processed: 219 average time/residue: 0.1121 time to fit residues: 39.0590 Evaluate side-chains 170 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 119 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 172 optimal weight: 30.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS D 630 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.049662 restraints weight = 71094.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.051528 restraints weight = 41077.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.052833 restraints weight = 28621.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.053691 restraints weight = 22411.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.054353 restraints weight = 19080.168| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17044 Z= 0.143 Angle : 0.684 18.546 23339 Z= 0.325 Chirality : 0.046 0.413 2879 Planarity : 0.004 0.056 2788 Dihedral : 4.789 27.857 2073 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.20), residues: 1894 helix: 0.34 (0.27), residues: 423 sheet: -0.13 (0.22), residues: 561 loop : -0.58 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 19 TYR 0.012 0.001 TYR C 217 PHE 0.014 0.001 PHE E 176 TRP 0.047 0.002 TRP A 69 HIS 0.008 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (16905) covalent geometry : angle 0.62146 / 0.31 (22962) SS BOND : bond 0.00318 / 0.20 ( 34) SS BOND : angle 1.22921 / 0.76 ( 68) hydrogen bonds : bond 0.03866 / 2.67 ( 460) hydrogen bonds : angle 5.03254 / 3.62 ( 1200) Misc. bond : bond 0.00238 / 0.12 ( 2) link_ALPHA1-3 : bond 0.00480 / 0.25 ( 7) link_ALPHA1-3 : angle 1.84596 / 1.22 ( 21) link_ALPHA1-6 : bond 0.00442 / 0.22 ( 7) link_ALPHA1-6 : angle 1.44085 / 0.92 ( 21) link_BETA1-4 : bond 0.00591 / 0.44 ( 34) link_BETA1-4 : angle 2.17794 / 1.45 ( 102) link_NAG-ASN : bond 0.00472 / 0.32 ( 55) link_NAG-ASN : angle 2.84612 / 2.29 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.493 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 100 MET cc_start: 0.9642 (mmm) cc_final: 0.9419 (mmm) REVERT: A 104 MET cc_start: 0.9422 (ttt) cc_final: 0.8861 (ttt) REVERT: A 180 ASP cc_start: 0.8683 (m-30) cc_final: 0.8031 (m-30) REVERT: A 374 HIS cc_start: 0.8133 (t70) cc_final: 0.7218 (t70) REVERT: C 53 PHE cc_start: 0.8207 (m-10) cc_final: 0.7790 (m-10) REVERT: C 111 LEU cc_start: 0.9411 (mm) cc_final: 0.9073 (mt) REVERT: C 116 LEU cc_start: 0.9461 (tt) cc_final: 0.9153 (mt) REVERT: C 207 LYS cc_start: 0.8473 (pttt) cc_final: 0.8197 (tptt) REVERT: C 210 PHE cc_start: 0.8963 (m-80) cc_final: 0.8615 (m-10) REVERT: D 584 GLU cc_start: 0.9156 (tp30) cc_final: 0.8293 (tm-30) REVERT: D 655 LYS cc_start: 0.8837 (mmpt) cc_final: 0.8466 (ptpt) REVERT: D 657 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8400 (mt-10) REVERT: E 92 GLU cc_start: 0.8718 (tt0) cc_final: 0.8492 (tt0) REVERT: E 95 MET cc_start: 0.8563 (mmp) cc_final: 0.8127 (mmm) REVERT: E 180 ASP cc_start: 0.8934 (m-30) cc_final: 0.8226 (m-30) REVERT: E 479 TRP cc_start: 0.8570 (m-90) cc_final: 0.8226 (m-90) REVERT: F 576 LEU cc_start: 0.8599 (mt) cc_final: 0.8024 (tt) REVERT: F 584 GLU cc_start: 0.8508 (tp30) cc_final: 0.7959 (tm-30) REVERT: F 591 GLN cc_start: 0.9512 (tt0) cc_final: 0.8968 (tt0) REVERT: F 601 LYS cc_start: 0.8839 (tptt) cc_final: 0.8279 (tppp) REVERT: F 647 GLU cc_start: 0.8396 (pt0) cc_final: 0.8023 (pt0) REVERT: F 655 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8477 (mmmt) REVERT: B 591 GLN cc_start: 0.9314 (tp40) cc_final: 0.8877 (tp40) REVERT: B 601 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8701 (mmmm) REVERT: L 49 TYR cc_start: 0.8993 (p90) cc_final: 0.8060 (p90) REVERT: L 53 ASN cc_start: 0.8654 (m-40) cc_final: 0.8154 (t0) REVERT: L 91 TYR cc_start: 0.7621 (t80) cc_final: 0.7346 (t80) REVERT: L 98 PHE cc_start: 0.7914 (m-10) cc_final: 0.7642 (m-10) REVERT: H 68 THR cc_start: 0.8841 (m) cc_final: 0.8449 (p) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1175 time to fit residues: 39.4381 Evaluate side-chains 161 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 34 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 67 optimal weight: 0.0570 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN D 630 GLN E 85 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.066937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.050735 restraints weight = 70544.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.052621 restraints weight = 40800.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.053927 restraints weight = 28342.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.054850 restraints weight = 22210.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.055417 restraints weight = 18734.178| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17044 Z= 0.118 Angle : 0.662 18.522 23339 Z= 0.317 Chirality : 0.046 0.407 2879 Planarity : 0.004 0.055 2788 Dihedral : 4.690 26.467 2073 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.20), residues: 1894 helix: 0.18 (0.26), residues: 429 sheet: -0.07 (0.22), residues: 550 loop : -0.58 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 186 TYR 0.010 0.001 TYR E 484 PHE 0.012 0.001 PHE E 176 TRP 0.031 0.002 TRP A 69 HIS 0.011 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (16905) covalent geometry : angle 0.60413 / 0.30 (22962) SS BOND : bond 0.00273 / 0.17 ( 34) SS BOND : angle 1.12092 / 0.70 ( 68) hydrogen bonds : bond 0.03870 / 2.63 ( 460) hydrogen bonds : angle 4.98646 / 3.58 ( 1200) Misc. bond : bond 0.00277 / 0.14 ( 2) link_ALPHA1-3 : bond 0.00505 / 0.27 ( 7) link_ALPHA1-3 : angle 1.80687 / 1.20 ( 21) link_ALPHA1-6 : bond 0.00471 / 0.23 ( 7) link_ALPHA1-6 : angle 1.41424 / 0.91 ( 21) link_BETA1-4 : bond 0.00634 / 0.47 ( 34) link_BETA1-4 : angle 2.08756 / 1.38 ( 102) link_NAG-ASN : bond 0.00491 / 0.33 ( 55) link_NAG-ASN : angle 2.71358 / 2.16 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8658 (m-30) cc_final: 0.7987 (m-30) REVERT: A 374 HIS cc_start: 0.8026 (t70) cc_final: 0.7169 (t70) REVERT: C 104 MET cc_start: 0.8956 (tmm) cc_final: 0.8754 (tmm) REVERT: C 111 LEU cc_start: 0.9392 (mm) cc_final: 0.9039 (mt) REVERT: C 116 LEU cc_start: 0.9392 (tt) cc_final: 0.9163 (mt) REVERT: C 207 LYS cc_start: 0.8472 (pttt) cc_final: 0.8151 (tptt) REVERT: C 210 PHE cc_start: 0.8938 (m-80) cc_final: 0.8661 (m-10) REVERT: D 584 GLU cc_start: 0.9101 (tp30) cc_final: 0.8242 (tm-30) REVERT: D 648 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8391 (pp20) REVERT: D 655 LYS cc_start: 0.8781 (mmpt) cc_final: 0.8518 (ptpp) REVERT: D 657 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8339 (mt-10) REVERT: E 95 MET cc_start: 0.8468 (mmp) cc_final: 0.8050 (mmm) REVERT: E 112 TRP cc_start: 0.8655 (m100) cc_final: 0.7903 (m100) REVERT: E 180 ASP cc_start: 0.8862 (m-30) cc_final: 0.8096 (m-30) REVERT: E 426 MET cc_start: 0.7229 (ttp) cc_final: 0.6901 (ttp) REVERT: F 576 LEU cc_start: 0.8581 (mt) cc_final: 0.8008 (tt) REVERT: F 584 GLU cc_start: 0.8510 (tp30) cc_final: 0.7989 (tm-30) REVERT: F 601 LYS cc_start: 0.8858 (tptt) cc_final: 0.8309 (tppp) REVERT: F 647 GLU cc_start: 0.8334 (pt0) cc_final: 0.7983 (pt0) REVERT: B 540 GLN cc_start: 0.9047 (mm110) cc_final: 0.7726 (mt0) REVERT: B 591 GLN cc_start: 0.9294 (tp40) cc_final: 0.8877 (tp40) REVERT: L 49 TYR cc_start: 0.9042 (p90) cc_final: 0.8836 (p90) REVERT: L 75 ILE cc_start: 0.8561 (mt) cc_final: 0.8340 (tt) REVERT: L 91 TYR cc_start: 0.7603 (t80) cc_final: 0.6923 (t80) REVERT: L 98 PHE cc_start: 0.7940 (m-10) cc_final: 0.7670 (m-10) REVERT: H 68 THR cc_start: 0.8835 (m) cc_final: 0.8464 (p) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1212 time to fit residues: 40.9411 Evaluate side-chains 155 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.0570 chunk 18 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN C 478 ASN D 630 GLN E 85 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.064893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.048715 restraints weight = 71832.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.050490 restraints weight = 42300.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.051726 restraints weight = 29833.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.052584 restraints weight = 23606.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053166 restraints weight = 20103.053| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17044 Z= 0.200 Angle : 0.741 17.988 23339 Z= 0.353 Chirality : 0.047 0.408 2879 Planarity : 0.004 0.053 2788 Dihedral : 4.843 30.287 2073 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1894 helix: 0.20 (0.26), residues: 423 sheet: -0.25 (0.22), residues: 547 loop : -0.60 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 186 TYR 0.014 0.002 TYR E 384 PHE 0.029 0.002 PHE E 233 TRP 0.036 0.002 TRP A 69 HIS 0.010 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (16905) covalent geometry : angle 0.68226 / 0.34 (22962) SS BOND : bond 0.00458 / 0.28 ( 34) SS BOND : angle 1.38436 / 0.90 ( 68) hydrogen bonds : bond 0.04066 / 2.82 ( 460) hydrogen bonds : angle 5.15565 / 3.69 ( 1200) Misc. bond : bond 0.00294 / 0.15 ( 2) link_ALPHA1-3 : bond 0.00417 / 0.21 ( 7) link_ALPHA1-3 : angle 1.88867 / 1.23 ( 21) link_ALPHA1-6 : bond 0.00384 / 0.20 ( 7) link_ALPHA1-6 : angle 1.47715 / 0.94 ( 21) link_BETA1-4 : bond 0.00552 / 0.41 ( 34) link_BETA1-4 : angle 2.19809 / 1.47 ( 102) link_NAG-ASN : bond 0.00509 / 0.35 ( 55) link_NAG-ASN : angle 2.90490 / 2.24 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.653 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 374 HIS cc_start: 0.8122 (t70) cc_final: 0.7317 (t70) REVERT: A 434 MET cc_start: 0.8678 (ttm) cc_final: 0.8282 (ttm) REVERT: C 104 MET cc_start: 0.9117 (tmm) cc_final: 0.8789 (tmm) REVERT: C 111 LEU cc_start: 0.9510 (mm) cc_final: 0.9131 (mt) REVERT: C 116 LEU cc_start: 0.9407 (tt) cc_final: 0.9175 (mt) REVERT: C 207 LYS cc_start: 0.8613 (pttt) cc_final: 0.8266 (tptt) REVERT: C 210 PHE cc_start: 0.9002 (m-80) cc_final: 0.8678 (m-10) REVERT: D 584 GLU cc_start: 0.9199 (tp30) cc_final: 0.8382 (tm-30) REVERT: D 648 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8363 (pp20) REVERT: D 655 LYS cc_start: 0.8812 (mmpt) cc_final: 0.8490 (ptpp) REVERT: D 657 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8350 (mt-10) REVERT: E 180 ASP cc_start: 0.8850 (m-30) cc_final: 0.8183 (m-30) REVERT: E 479 TRP cc_start: 0.8614 (m-90) cc_final: 0.8398 (m-10) REVERT: F 576 LEU cc_start: 0.8634 (mt) cc_final: 0.8038 (tt) REVERT: F 584 GLU cc_start: 0.8562 (tp30) cc_final: 0.7862 (tm-30) REVERT: F 591 GLN cc_start: 0.9379 (tt0) cc_final: 0.8928 (tt0) REVERT: F 601 LYS cc_start: 0.8918 (tptt) cc_final: 0.8383 (tppp) REVERT: F 625 ASN cc_start: 0.8643 (t0) cc_final: 0.8407 (t0) REVERT: F 647 GLU cc_start: 0.8403 (pt0) cc_final: 0.8046 (pt0) REVERT: F 655 LYS cc_start: 0.8726 (mmpt) cc_final: 0.8525 (mmmt) REVERT: B 591 GLN cc_start: 0.9311 (tp40) cc_final: 0.8845 (tp40) REVERT: B 601 LYS cc_start: 0.8921 (mmtm) cc_final: 0.8626 (mmmm) REVERT: L 53 ASN cc_start: 0.8999 (m110) cc_final: 0.8635 (m110) REVERT: L 75 ILE cc_start: 0.8568 (mt) cc_final: 0.8336 (mt) REVERT: L 82 ASP cc_start: 0.6450 (m-30) cc_final: 0.5964 (m-30) REVERT: L 91 TYR cc_start: 0.7165 (t80) cc_final: 0.6563 (t80) REVERT: H 67 PHE cc_start: 0.8026 (m-10) cc_final: 0.7767 (m-10) REVERT: H 68 THR cc_start: 0.8905 (m) cc_final: 0.8488 (p) REVERT: H 100 TYR cc_start: 0.9051 (m-80) cc_final: 0.8837 (m-80) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1277 time to fit residues: 40.1203 Evaluate side-chains 148 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 96 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** 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 = 0.3267 r_free = 0.3267 target = 0.066390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.050358 restraints weight = 69719.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.052192 restraints weight = 40314.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.053490 restraints weight = 28053.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.054391 restraints weight = 21955.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.054997 restraints weight = 18502.066| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17044 Z= 0.121 Angle : 0.667 18.349 23339 Z= 0.319 Chirality : 0.046 0.402 2879 Planarity : 0.004 0.052 2788 Dihedral : 4.726 27.918 2073 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.20), residues: 1894 helix: 0.28 (0.26), residues: 423 sheet: -0.13 (0.22), residues: 547 loop : -0.57 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 186 TYR 0.011 0.001 TYR H 100N PHE 0.025 0.001 PHE E 233 TRP 0.037 0.002 TRP A 69 HIS 0.010 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (16905) covalent geometry : angle 0.60797 / 0.31 (22962) SS BOND : bond 0.00299 / 0.19 ( 34) SS BOND : angle 1.19769 / 0.77 ( 68) hydrogen bonds : bond 0.03822 / 2.62 ( 460) hydrogen bonds : angle 4.98907 / 3.57 ( 1200) Misc. bond : bond 0.00371 / 0.19 ( 2) link_ALPHA1-3 : bond 0.00487 / 0.26 ( 7) link_ALPHA1-3 : angle 1.80632 / 1.20 ( 21) link_ALPHA1-6 : bond 0.00454 / 0.23 ( 7) link_ALPHA1-6 : angle 1.42175 / 0.91 ( 21) link_BETA1-4 : bond 0.00615 / 0.46 ( 34) link_BETA1-4 : angle 2.05046 / 1.36 ( 102) link_NAG-ASN : bond 0.00489 / 0.33 ( 55) link_NAG-ASN : angle 2.74471 / 2.14 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2428.71 seconds wall clock time: 43 minutes 10.51 seconds (2590.51 seconds total)