Starting phenix.real_space_refine on Sat Jul 4 12:08:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7txd_26157/07_2026/7txd_26157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7txd_26157/07_2026/7txd_26157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7txd_26157/07_2026/7txd_26157.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7txd_26157/07_2026/7txd_26157.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7txd_26157/07_2026/7txd_26157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7txd_26157/07_2026/7txd_26157.map" model { file = "/net/cci-nas-00/data/ceres_data/7txd_26157/07_2026/7txd_26157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7txd_26157/07_2026/7txd_26157.cif" } resolution = 3.87 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= 0.004 sd= 0.032 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 105 5.16 5 C 12854 2.51 5 N 3463 2.21 5 O 4133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s 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: 20555 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3101 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 22, 'TRANS': 374} Chain breaks: 2 Chain: "B" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1004 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3101 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 22, 'TRANS': 374} Chain breaks: 2 Chain: "D" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 900 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3101 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 22, 'TRANS': 374} Chain breaks: 2 Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "H" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "I" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "J" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1002 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "K" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1002 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "L" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1002 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "M" 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 Time building chain proxies: 4.95, per 1000 atoms: 0.24 Number of scatterers: 20555 At special positions: 0 Unit cell: (126.26, 188.32, 185.11, 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 105 16.00 O 4133 8.00 N 3463 7.00 C 12854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " 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=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.07 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.03 Simple disulfide: pdb=" SG CYS G 130 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 84 " distance=2.03 Simple disulfide: pdb=" SG CYS H 130 " - pdb=" SG CYS H 159 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.03 Simple disulfide: pdb=" SG CYS I 130 " - pdb=" SG CYS I 159 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA V 3 " - " MAN V 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " BMA V 3 " - " MAN V 5 " " BMA b 3 " - " MAN b 7 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 295 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 332 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 462 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG C 601 " - " ASN C 355 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 88 " " NAG C 604 " - " ASN C 295 " " NAG C 605 " - " ASN C 332 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 301 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG D 703 " - " ASN D 618 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 332 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 462 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 234 " " NAG E 608 " - " ASN E 339 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 625 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 448 " " NAG P 1 " - " ASN A 363 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 355 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 448 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 363 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 448 " " NAG e 1 " - " ASN E 276 " " NAG f 1 " - " ASN E 363 " " NAG g 1 " - " ASN E 392 " " NAG h 1 " - " ASN F 611 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 837.5 milliseconds 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 35 sheets defined 31.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 100 through 116 removed outlier: 4.557A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 326 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.687A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 520 removed outlier: 4.047A pdb=" N LEU B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 543 removed outlier: 3.853A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 removed outlier: 3.502A pdb=" N THR B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 4.088A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 4.295A pdb=" N SER B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.952A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'C' and resid 64 through 74 Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.868A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.597A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 474 through 481 removed outlier: 3.639A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.717A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 594 removed outlier: 3.714A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.164A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.529A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 655 Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.732A pdb=" N GLN E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 327 removed outlier: 3.513A pdb=" N ILE E 326 " --> pdb=" O ILE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.650A pdb=" N GLN E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 483 removed outlier: 3.654A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 523 removed outlier: 3.835A pdb=" N LEU F 523 " --> pdb=" O PHE F 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 519 through 523' Processing helix chain 'F' and resid 529 through 542 removed outlier: 3.852A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 596 Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.612A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 618 through 623' Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.670A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP F 632 " --> pdb=" O TRP F 628 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 657 removed outlier: 3.663A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.569A pdb=" N LEU G 61 " --> pdb=" O ARG G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 79 removed outlier: 3.550A pdb=" N SER G 79 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 154 Processing helix chain 'H' and resid 58 through 62 removed outlier: 3.602A pdb=" N TRP H 62 " --> pdb=" O ARG H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 removed outlier: 3.556A pdb=" N ASP H 78 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER H 79 " --> pdb=" O ILE H 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 75 through 79' Processing helix chain 'H' and resid 150 through 154 removed outlier: 3.510A pdb=" N SER H 154 " --> pdb=" O LEU H 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 62 removed outlier: 3.698A pdb=" N LEU I 61 " --> pdb=" O ARG I 58 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP I 62 " --> pdb=" O ARG I 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 58 through 62' Processing helix chain 'I' and resid 75 through 79 Processing helix chain 'I' and resid 150 through 154 removed outlier: 3.511A pdb=" N SER I 154 " --> pdb=" O LEU I 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 48 Processing helix chain 'J' and resid 49 through 60 Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.849A pdb=" N LEU J 76 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY J 81 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 105 through 113 removed outlier: 3.575A pdb=" N LYS J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 125 Processing helix chain 'J' and resid 138 through 146 Processing helix chain 'J' and resid 148 through 161 removed outlier: 3.761A pdb=" N ALA J 152 " --> pdb=" O ASN J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 47 removed outlier: 3.748A pdb=" N LEU K 43 " --> pdb=" O THR K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 removed outlier: 3.797A pdb=" N VAL K 53 " --> pdb=" O HIS K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.634A pdb=" N LEU K 76 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET K 80 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY K 81 " --> pdb=" O ALA K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 92 removed outlier: 3.524A pdb=" N VAL K 86 " --> pdb=" O HIS K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 113 removed outlier: 4.094A pdb=" N LYS K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 126 Processing helix chain 'K' and resid 138 through 146 Processing helix chain 'K' and resid 148 through 161 removed outlier: 3.589A pdb=" N ALA K 152 " --> pdb=" O ASN K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 48 Processing helix chain 'L' and resid 49 through 60 removed outlier: 3.567A pdb=" N VAL L 53 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 80 removed outlier: 3.596A pdb=" N LEU L 76 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET L 80 " --> pdb=" O LEU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 92 removed outlier: 3.716A pdb=" N VAL L 86 " --> pdb=" O HIS L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 113 removed outlier: 3.533A pdb=" N LEU L 109 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS L 113 " --> pdb=" O LEU L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 125 Processing helix chain 'L' and resid 138 through 146 Processing helix chain 'L' and resid 148 through 161 removed outlier: 3.506A pdb=" N ALA L 152 " --> pdb=" O ASN L 148 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL L 154 " --> pdb=" O ASP L 150 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU L 161 " --> pdb=" O LYS L 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.091A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.733A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 202 Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 39 removed outlier: 3.567A pdb=" N THR C 37 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.517A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.862A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.004A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 196 through 202 removed outlier: 3.590A pdb=" N LEU C 125 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 424 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.508A pdb=" N GLN C 287 " --> pdb=" O MET C 271 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 259 through 260 removed outlier: 4.407A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.638A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.194A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.885A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 196 through 202 Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 260 Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 260 removed outlier: 3.727A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 413 through 417 removed outlier: 4.293A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR E 297 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 366 through 367 removed outlier: 3.670A pdb=" N GLY E 366 " --> pdb=" O LYS I 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 374 through 378 Processing sheet with id=AC6, first strand: chain 'G' and resid 2 through 5 removed outlier: 4.236A pdb=" N LYS G 2 " --> pdb=" O GLU G 92 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP G 28 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN G 40 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE G 43 " --> pdb=" O GLN G 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 12 through 14 removed outlier: 3.637A pdb=" N VAL G 12 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 71 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 99 through 102 removed outlier: 6.346A pdb=" N GLN G 112 " --> pdb=" O GLN G 148 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN G 148 " --> pdb=" O GLN G 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 127 through 131 Processing sheet with id=AD1, first strand: chain 'H' and resid 2 through 5 removed outlier: 4.213A pdb=" N LYS H 2 " --> pdb=" O GLU H 92 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS H 29 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP H 28 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN H 40 " --> pdb=" O PHE H 43 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE H 43 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AD3, first strand: chain 'H' and resid 99 through 102 removed outlier: 3.511A pdb=" N GLY H 99 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN H 112 " --> pdb=" O GLN H 148 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN H 148 " --> pdb=" O GLN H 112 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 138 through 139 Processing sheet with id=AD5, first strand: chain 'I' and resid 2 through 6 removed outlier: 4.057A pdb=" N LYS I 2 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS I 29 " --> pdb=" O ILE I 83 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP I 28 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AD7, first strand: chain 'I' and resid 99 through 102 Processing sheet with id=AD8, first strand: chain 'I' and resid 138 through 139 724 hydrogen bonds defined for protein. 1977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 6568 1.35 - 1.50: 5501 1.50 - 1.65: 8710 1.65 - 1.80: 44 1.80 - 1.94: 94 Bond restraints: 20917 Sorted by residual: bond pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " ideal model delta sigma weight residual 1.808 1.945 -0.137 3.30e-02 9.18e+02 1.72e+01 bond pdb=" C1 NAG F 702 " pdb=" O5 NAG F 702 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C3 BMA V 3 " pdb=" O3 BMA V 3 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" N LYS A 502 " pdb=" CA LYS A 502 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.29e-02 6.01e+03 1.13e+01 bond pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 1.808 1.705 0.103 3.30e-02 9.18e+02 9.76e+00 ... (remaining 20912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.57: 28156 4.57 - 9.14: 205 9.14 - 13.71: 17 13.71 - 18.28: 1 18.28 - 22.85: 1 Bond angle restraints: 28380 Sorted by residual: angle pdb=" CA CYS A 296 " pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 114.40 137.25 -22.85 2.30e+00 1.89e-01 9.87e+01 angle pdb=" CA ASN C 99 " pdb=" CB ASN C 99 " pdb=" CG ASN C 99 " ideal model delta sigma weight residual 112.60 106.74 5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" N CYS A 296 " pdb=" CA CYS A 296 " pdb=" C CYS A 296 " ideal model delta sigma weight residual 108.99 118.12 -9.13 1.57e+00 4.06e-01 3.38e+01 angle pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 114.40 127.48 -13.08 2.30e+00 1.89e-01 3.24e+01 angle pdb=" N ASN A 99 " pdb=" CA ASN A 99 " pdb=" C ASN A 99 " ideal model delta sigma weight residual 113.18 106.84 6.34 1.21e+00 6.83e-01 2.75e+01 ... (remaining 28375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.19: 10923 18.19 - 36.38: 800 36.38 - 54.56: 126 54.56 - 72.75: 23 72.75 - 90.94: 26 Dihedral angle restraints: 11898 sinusoidal: 4784 harmonic: 7114 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -168.98 82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS E 228 " pdb=" SG CYS E 228 " pdb=" SG CYS E 239 " pdb=" CB CYS E 239 " ideal model delta sinusoidal sigma weight residual 93.00 166.11 -73.11 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 165.00 -72.00 1 1.00e+01 1.00e-02 6.63e+01 ... (remaining 11895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3058 0.090 - 0.180: 426 0.180 - 0.269: 39 0.269 - 0.359: 13 0.359 - 0.449: 5 Chirality restraints: 3541 Sorted by residual: chirality pdb=" CB ILE F 603 " pdb=" CA ILE F 603 " pdb=" CG1 ILE F 603 " pdb=" CG2 ILE F 603 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.44e+00 chirality pdb=" C1 NAG C 606 " pdb=" ND2 ASN C 392 " pdb=" C2 NAG C 606 " pdb=" O5 NAG C 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 3538 not shown) Planarity restraints: 3551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 1 " -0.261 2.00e-02 2.50e+03 2.22e-01 6.14e+02 pdb=" C7 NAG h 1 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG h 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG h 1 " 0.381 2.00e-02 2.50e+03 pdb=" O7 NAG h 1 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 703 " 0.167 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C7 NAG F 703 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG F 703 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG F 703 " -0.224 2.00e-02 2.50e+03 pdb=" O7 NAG F 703 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " -0.096 2.00e-02 2.50e+03 7.97e-02 7.94e+01 pdb=" C7 NAG h 2 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " -0.073 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " 0.127 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " 0.016 2.00e-02 2.50e+03 ... (remaining 3548 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5118 2.81 - 3.33: 17730 3.33 - 3.85: 32834 3.85 - 4.38: 35559 4.38 - 4.90: 62132 Nonbonded interactions: 153373 Sorted by model distance: nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.287 3.040 nonbonded pdb=" OG SER A 365 " pdb=" O LYS G 46 " model vdw 2.301 3.040 nonbonded pdb=" OD2 ASP C 107 " pdb=" OH TYR C 217 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" O CYS B 604 " model vdw 2.309 3.040 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.311 3.040 ... (remaining 153368 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 33 through 606) selection = (chain 'E' and resid 33 through 606) } ncs_group { reference = (chain 'B' and ((resid 522 through 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 542 or resid 564 through 655 or resid 701 t \ hrough 703)) selection = chain 'D' selection = (chain 'F' and ((resid 522 through 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 542 or resid 564 through 655 or resid 701 t \ hrough 703)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'b' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'h' } 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.710 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.006 0.137 21048 Z= 0.313 Angle : 1.098 22.845 28737 Z= 0.548 Chirality : 0.062 0.449 3541 Planarity : 0.008 0.222 3499 Dihedral : 13.232 90.940 7180 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.04 % 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: -2.19 (0.15), residues: 2441 helix: -1.69 (0.17), residues: 682 sheet: -0.32 (0.24), residues: 475 loop : -1.74 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG H 54 TYR 0.020 0.002 TYR E 435 PHE 0.028 0.002 PHE H 26 TRP 0.045 0.002 TRP C 112 HIS 0.014 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.31 (20917) covalent geometry : angle 1.05594 / 0.54 (28380) SS BOND : bond 0.00730 / 0.35 ( 36) SS BOND : angle 2.03772 / 1.32 ( 72) hydrogen bonds : bond 0.17028 / 11.37 ( 720) hydrogen bonds : angle 7.24077 / 4.96 ( 1977) link_ALPHA1-2 : bond 0.00215 / 0.11 ( 4) link_ALPHA1-2 : angle 2.51570 / 1.82 ( 12) link_ALPHA1-3 : bond 0.00791 / 0.38 ( 3) link_ALPHA1-3 : angle 2.97069 / 1.29 ( 9) link_ALPHA1-6 : bond 0.00450 / 0.22 ( 3) link_ALPHA1-6 : angle 1.41923 / 1.00 ( 9) link_BETA1-4 : bond 0.00847 / 0.52 ( 33) link_BETA1-4 : angle 2.57942 / 1.72 ( 99) link_NAG-ASN : bond 0.00822 / 0.45 ( 52) link_NAG-ASN : angle 3.44349 / 2.44 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8409 (p90) cc_final: 0.6374 (m-10) REVERT: A 236 THR cc_start: 0.7999 (p) cc_final: 0.7717 (p) REVERT: A 321 ASP cc_start: 0.8286 (m-30) cc_final: 0.8021 (m-30) REVERT: A 426 MET cc_start: 0.7525 (mtm) cc_final: 0.7185 (mtm) REVERT: B 529 THR cc_start: 0.8008 (m) cc_final: 0.7578 (p) REVERT: B 589 ASP cc_start: 0.8668 (t0) cc_final: 0.8035 (t0) REVERT: D 621 GLU cc_start: 0.8313 (pm20) cc_final: 0.8066 (pm20) REVERT: F 591 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8154 (tm-30) REVERT: F 599 SER cc_start: 0.7961 (p) cc_final: 0.7750 (p) REVERT: F 647 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7667 (tm-30) REVERT: G 91 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6532 (tm-30) REVERT: G 95 LEU cc_start: 0.8793 (tp) cc_final: 0.8484 (tp) REVERT: H 91 GLU cc_start: 0.6700 (tm-30) cc_final: 0.6440 (tm-30) REVERT: I 70 ILE cc_start: 0.8662 (mm) cc_final: 0.8435 (mt) REVERT: I 169 GLU cc_start: 0.9126 (pt0) cc_final: 0.8737 (mp0) REVERT: J 54 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8120 (pt0) REVERT: J 66 ARG cc_start: 0.7293 (mpt180) cc_final: 0.6644 (tpp80) REVERT: K 105 THR cc_start: 0.7696 (p) cc_final: 0.7070 (p) REVERT: K 108 HIS cc_start: 0.7117 (m90) cc_final: 0.6614 (t70) REVERT: K 150 ASP cc_start: 0.8340 (t0) cc_final: 0.7993 (m-30) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1344 time to fit residues: 78.4583 Evaluate side-chains 255 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 590 GLN C 114 GLN C 197 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.111598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.080023 restraints weight = 53588.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.080598 restraints weight = 33581.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.081958 restraints weight = 24004.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.082091 restraints weight = 19601.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.082180 restraints weight = 18126.267| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 21048 Z= 0.362 Angle : 0.868 12.132 28737 Z= 0.427 Chirality : 0.050 0.319 3541 Planarity : 0.005 0.054 3499 Dihedral : 4.836 23.588 2591 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.12 % Rotamer: Outliers : 1.77 % Allowed : 11.10 % Favored : 87.13 % 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: -1.54 (0.16), residues: 2441 helix: -0.40 (0.19), residues: 704 sheet: -0.58 (0.22), residues: 505 loop : -1.57 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 54 TYR 0.032 0.003 TYR E 384 PHE 0.024 0.003 PHE A 233 TRP 0.022 0.002 TRP C 112 HIS 0.009 0.002 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.36 (20917) covalent geometry : angle 0.82525 / 0.42 (28380) SS BOND : bond 0.00570 / 0.36 ( 36) SS BOND : angle 1.68513 / 1.07 ( 72) hydrogen bonds : bond 0.05276 / 3.53 ( 720) hydrogen bonds : angle 6.00364 / 4.14 ( 1977) link_ALPHA1-2 : bond 0.00353 / 0.18 ( 4) link_ALPHA1-2 : angle 2.02070 / 1.48 ( 12) link_ALPHA1-3 : bond 0.00259 / 0.13 ( 3) link_ALPHA1-3 : angle 2.19394 / 1.17 ( 9) link_ALPHA1-6 : bond 0.00117 / 0.06 ( 3) link_ALPHA1-6 : angle 1.91008 / 1.22 ( 9) link_BETA1-4 : bond 0.00551 / 0.38 ( 33) link_BETA1-4 : angle 2.27516 / 1.59 ( 99) link_NAG-ASN : bond 0.00776 / 0.48 ( 52) link_NAG-ASN : angle 3.07412 / 2.18 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8849 (p90) cc_final: 0.6672 (m-10) REVERT: A 368 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8487 (t70) REVERT: A 446 VAL cc_start: 0.8716 (t) cc_final: 0.8441 (p) REVERT: A 492 GLU cc_start: 0.8216 (tt0) cc_final: 0.7873 (tt0) REVERT: B 589 ASP cc_start: 0.9227 (t0) cc_final: 0.8635 (t0) REVERT: C 479 TRP cc_start: 0.8532 (m-10) cc_final: 0.8069 (m-90) REVERT: D 530 MET cc_start: 0.6484 (mmt) cc_final: 0.5987 (mmt) REVERT: F 591 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8537 (tm-30) REVERT: F 647 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8384 (tm-30) REVERT: G 78 ASP cc_start: 0.8593 (m-30) cc_final: 0.8238 (m-30) REVERT: H 96 LEU cc_start: 0.8793 (tt) cc_final: 0.8317 (mm) REVERT: I 169 GLU cc_start: 0.9258 (pt0) cc_final: 0.8782 (mp0) REVERT: J 54 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8268 (pt0) REVERT: J 66 ARG cc_start: 0.7279 (mpt180) cc_final: 0.6900 (tpp80) REVERT: K 108 HIS cc_start: 0.7343 (m90) cc_final: 0.7132 (t70) REVERT: L 87 GLU cc_start: 0.8726 (pp20) cc_final: 0.8504 (pp20) REVERT: L 91 LYS cc_start: 0.8535 (mmtt) cc_final: 0.8334 (mmtm) REVERT: L 156 GLN cc_start: 0.8533 (pp30) cc_final: 0.8243 (pp30) outliers start: 38 outliers final: 26 residues processed: 282 average time/residue: 0.1384 time to fit residues: 62.4666 Evaluate side-chains 247 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 30 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 72 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 224 optimal weight: 20.0000 chunk 113 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 231 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN B 543 ASN J 49 HIS J 125 HIS ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.115886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.084715 restraints weight = 52704.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.086279 restraints weight = 30579.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.086963 restraints weight = 22309.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.087159 restraints weight = 19719.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.087284 restraints weight = 17628.268| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 21048 Z= 0.118 Angle : 0.637 12.237 28737 Z= 0.304 Chirality : 0.044 0.301 3541 Planarity : 0.004 0.050 3499 Dihedral : 4.312 22.334 2591 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.31 % Allowed : 13.53 % Favored : 85.17 % 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: -1.05 (0.16), residues: 2441 helix: 0.31 (0.20), residues: 696 sheet: -0.47 (0.22), residues: 504 loop : -1.37 (0.16), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.012 0.001 TYR A 435 PHE 0.024 0.001 PHE L 135 TRP 0.021 0.001 TRP C 112 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (20917) covalent geometry : angle 0.59227 / 0.29 (28380) SS BOND : bond 0.00404 / 0.21 ( 36) SS BOND : angle 1.34357 / 0.83 ( 72) hydrogen bonds : bond 0.03859 / 2.56 ( 720) hydrogen bonds : angle 5.38467 / 3.72 ( 1977) link_ALPHA1-2 : bond 0.00172 / 0.09 ( 4) link_ALPHA1-2 : angle 1.95522 / 1.28 ( 12) link_ALPHA1-3 : bond 0.00660 / 0.33 ( 3) link_ALPHA1-3 : angle 1.88427 / 0.97 ( 9) link_ALPHA1-6 : bond 0.00457 / 0.23 ( 3) link_ALPHA1-6 : angle 1.48254 / 1.01 ( 9) link_BETA1-4 : bond 0.00503 / 0.32 ( 33) link_BETA1-4 : angle 1.86500 / 1.30 ( 99) link_NAG-ASN : bond 0.00477 / 0.25 ( 52) link_NAG-ASN : angle 2.68688 / 1.91 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 266 time to evaluate : 0.771 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 61 TYR cc_start: 0.8783 (p90) cc_final: 0.6642 (m-10) REVERT: A 446 VAL cc_start: 0.8606 (t) cc_final: 0.8364 (p) REVERT: A 492 GLU cc_start: 0.8222 (tt0) cc_final: 0.8016 (tt0) REVERT: B 589 ASP cc_start: 0.9196 (t0) cc_final: 0.8738 (t0) REVERT: C 479 TRP cc_start: 0.8332 (m-10) cc_final: 0.7746 (m-90) REVERT: D 530 MET cc_start: 0.6109 (mmt) cc_final: 0.5471 (mmt) REVERT: D 621 GLU cc_start: 0.8375 (pm20) cc_final: 0.7963 (pm20) REVERT: F 647 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8031 (tm-30) REVERT: H 62 TRP cc_start: 0.8142 (m-10) cc_final: 0.7701 (m-10) REVERT: H 96 LEU cc_start: 0.8763 (tt) cc_final: 0.8324 (mm) REVERT: I 88 ASP cc_start: 0.8423 (p0) cc_final: 0.8115 (p0) REVERT: I 169 GLU cc_start: 0.9272 (pt0) cc_final: 0.8747 (mp0) REVERT: I 172 ILE cc_start: 0.7738 (mm) cc_final: 0.6805 (pt) REVERT: J 54 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8153 (pt0) REVERT: J 66 ARG cc_start: 0.7214 (mpt180) cc_final: 0.6632 (tpp80) REVERT: J 155 LEU cc_start: 0.8956 (mm) cc_final: 0.8572 (tt) REVERT: K 108 HIS cc_start: 0.7342 (m90) cc_final: 0.7105 (t70) REVERT: L 91 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8336 (mmtm) REVERT: L 134 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7355 (pttm) outliers start: 28 outliers final: 17 residues processed: 284 average time/residue: 0.1301 time to fit residues: 60.3114 Evaluate side-chains 252 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 134 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 239 optimal weight: 0.0070 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.115072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.083014 restraints weight = 52806.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.084779 restraints weight = 30799.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.085600 restraints weight = 20681.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.086075 restraints weight = 17816.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.086288 restraints weight = 16248.979| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 21048 Z= 0.114 Angle : 0.620 13.053 28737 Z= 0.294 Chirality : 0.043 0.296 3541 Planarity : 0.003 0.045 3499 Dihedral : 4.096 22.174 2591 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.26 % Allowed : 15.67 % Favored : 83.07 % 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: -0.81 (0.16), residues: 2441 helix: 0.62 (0.20), residues: 700 sheet: -0.38 (0.22), residues: 504 loop : -1.27 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.013 0.001 TYR E 40 PHE 0.029 0.001 PHE H 26 TRP 0.016 0.001 TRP C 112 HIS 0.008 0.001 HIS K 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (20917) covalent geometry : angle 0.57837 / 0.28 (28380) SS BOND : bond 0.00398 / 0.21 ( 36) SS BOND : angle 1.29962 / 0.84 ( 72) hydrogen bonds : bond 0.03486 / 2.30 ( 720) hydrogen bonds : angle 5.14149 / 3.56 ( 1977) link_ALPHA1-2 : bond 0.00108 / 0.06 ( 4) link_ALPHA1-2 : angle 1.87512 / 1.25 ( 12) link_ALPHA1-3 : bond 0.00696 / 0.35 ( 3) link_ALPHA1-3 : angle 1.82547 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00456 / 0.23 ( 3) link_ALPHA1-6 : angle 1.44879 / 0.98 ( 9) link_BETA1-4 : bond 0.00461 / 0.29 ( 33) link_BETA1-4 : angle 1.79657 / 1.26 ( 99) link_NAG-ASN : bond 0.00459 / 0.24 ( 52) link_NAG-ASN : angle 2.54751 / 1.79 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 0.758 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 61 TYR cc_start: 0.8747 (p90) cc_final: 0.6593 (m-10) REVERT: A 102 GLU cc_start: 0.8483 (tp30) cc_final: 0.8124 (tp30) REVERT: A 321 ASP cc_start: 0.8284 (m-30) cc_final: 0.7986 (m-30) REVERT: A 446 VAL cc_start: 0.8540 (t) cc_final: 0.8310 (p) REVERT: B 589 ASP cc_start: 0.9239 (t0) cc_final: 0.8611 (t0) REVERT: C 479 TRP cc_start: 0.8299 (m-10) cc_final: 0.7713 (m-90) REVERT: D 530 MET cc_start: 0.5811 (mmt) cc_final: 0.5223 (mmt) REVERT: D 648 GLU cc_start: 0.8355 (pp20) cc_final: 0.8118 (pp20) REVERT: H 62 TRP cc_start: 0.8074 (m-10) cc_final: 0.7648 (m-10) REVERT: H 96 LEU cc_start: 0.8819 (tt) cc_final: 0.8405 (mm) REVERT: I 172 ILE cc_start: 0.7765 (mm) cc_final: 0.6923 (pt) REVERT: J 54 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8189 (pt0) REVERT: J 66 ARG cc_start: 0.7199 (mpt180) cc_final: 0.6581 (tpp80) REVERT: J 155 LEU cc_start: 0.8900 (mm) cc_final: 0.8653 (tt) REVERT: K 50 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8562 (mt) REVERT: K 108 HIS cc_start: 0.7413 (m90) cc_final: 0.7018 (t-170) REVERT: L 156 GLN cc_start: 0.8508 (pp30) cc_final: 0.8207 (pp30) outliers start: 27 outliers final: 15 residues processed: 275 average time/residue: 0.1258 time to fit residues: 56.5650 Evaluate side-chains 249 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 75 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 153 optimal weight: 3.9990 chunk 188 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN D 591 GLN G 164 ASN ** K 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.113060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081601 restraints weight = 52986.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.082312 restraints weight = 32205.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.083794 restraints weight = 22745.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083850 restraints weight = 18580.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.084066 restraints weight = 17313.980| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21048 Z= 0.161 Angle : 0.640 11.326 28737 Z= 0.306 Chirality : 0.044 0.297 3541 Planarity : 0.004 0.044 3499 Dihedral : 4.107 23.314 2591 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.68 % Allowed : 16.56 % Favored : 81.76 % 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: -0.72 (0.16), residues: 2441 helix: 0.81 (0.20), residues: 702 sheet: -0.39 (0.24), residues: 465 loop : -1.25 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 131 TYR 0.015 0.001 TYR E 40 PHE 0.029 0.002 PHE H 26 TRP 0.015 0.001 TRP D 631 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (20917) covalent geometry : angle 0.60045 / 0.30 (28380) SS BOND : bond 0.00389 / 0.21 ( 36) SS BOND : angle 1.28552 / 0.83 ( 72) hydrogen bonds : bond 0.03574 / 2.36 ( 720) hydrogen bonds : angle 5.07129 / 3.52 ( 1977) link_ALPHA1-2 : bond 0.00171 / 0.09 ( 4) link_ALPHA1-2 : angle 1.79302 / 1.20 ( 12) link_ALPHA1-3 : bond 0.00576 / 0.29 ( 3) link_ALPHA1-3 : angle 1.89275 / 0.96 ( 9) link_ALPHA1-6 : bond 0.00361 / 0.18 ( 3) link_ALPHA1-6 : angle 1.48674 / 1.00 ( 9) link_BETA1-4 : bond 0.00418 / 0.28 ( 33) link_BETA1-4 : angle 1.80338 / 1.27 ( 99) link_NAG-ASN : bond 0.00463 / 0.26 ( 52) link_NAG-ASN : angle 2.54545 / 1.78 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8745 (p90) cc_final: 0.6589 (m-10) REVERT: A 446 VAL cc_start: 0.8696 (t) cc_final: 0.8432 (p) REVERT: B 589 ASP cc_start: 0.9257 (t0) cc_final: 0.8627 (t0) REVERT: C 479 TRP cc_start: 0.8323 (m-10) cc_final: 0.7771 (m-90) REVERT: D 648 GLU cc_start: 0.8333 (pp20) cc_final: 0.8086 (pp20) REVERT: H 96 LEU cc_start: 0.8849 (tt) cc_final: 0.8477 (mm) REVERT: I 172 ILE cc_start: 0.7876 (mm) cc_final: 0.7575 (mt) REVERT: J 54 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8242 (pt0) REVERT: J 66 ARG cc_start: 0.7245 (mpt180) cc_final: 0.6666 (tpp80) REVERT: J 155 LEU cc_start: 0.8932 (mm) cc_final: 0.8601 (tp) REVERT: K 108 HIS cc_start: 0.7245 (m90) cc_final: 0.6982 (t-170) REVERT: K 123 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7584 (pp) REVERT: L 91 LYS cc_start: 0.8750 (mmtm) cc_final: 0.8368 (mmtm) outliers start: 36 outliers final: 26 residues processed: 274 average time/residue: 0.1307 time to fit residues: 58.0435 Evaluate side-chains 251 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 75 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 91 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN G 164 ASN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 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 = 0.3919 r_free = 0.3919 target = 0.113096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.081450 restraints weight = 52422.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.082301 restraints weight = 32131.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.083601 restraints weight = 22493.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.083781 restraints weight = 18770.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.083920 restraints weight = 17137.699| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21048 Z= 0.146 Angle : 0.632 10.523 28737 Z= 0.301 Chirality : 0.044 0.294 3541 Planarity : 0.003 0.043 3499 Dihedral : 4.078 23.081 2591 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.91 % Allowed : 17.02 % Favored : 81.06 % 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: -0.60 (0.17), residues: 2441 helix: 1.00 (0.20), residues: 703 sheet: -0.41 (0.24), residues: 465 loop : -1.19 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 131 TYR 0.014 0.001 TYR E 40 PHE 0.028 0.001 PHE H 26 TRP 0.014 0.001 TRP F 571 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (20917) covalent geometry : angle 0.59170 / 0.29 (28380) SS BOND : bond 0.00383 / 0.21 ( 36) SS BOND : angle 1.43197 / 0.89 ( 72) hydrogen bonds : bond 0.03481 / 2.30 ( 720) hydrogen bonds : angle 4.99849 / 3.48 ( 1977) link_ALPHA1-2 : bond 0.00143 / 0.07 ( 4) link_ALPHA1-2 : angle 1.76949 / 1.18 ( 12) link_ALPHA1-3 : bond 0.00589 / 0.29 ( 3) link_ALPHA1-3 : angle 1.86075 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00375 / 0.19 ( 3) link_ALPHA1-6 : angle 1.46928 / 0.99 ( 9) link_BETA1-4 : bond 0.00427 / 0.28 ( 33) link_BETA1-4 : angle 1.76132 / 1.24 ( 99) link_NAG-ASN : bond 0.00463 / 0.26 ( 52) link_NAG-ASN : angle 2.54073 / 1.77 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.810 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 61 TYR cc_start: 0.8738 (p90) cc_final: 0.6566 (m-10) REVERT: A 95 MET cc_start: 0.9140 (ppp) cc_final: 0.8934 (ppp) REVERT: A 446 VAL cc_start: 0.8678 (t) cc_final: 0.8402 (p) REVERT: B 589 ASP cc_start: 0.9257 (t0) cc_final: 0.8632 (t0) REVERT: C 479 TRP cc_start: 0.8315 (m-10) cc_final: 0.7758 (m-90) REVERT: E 295 ASN cc_start: 0.6884 (m-40) cc_final: 0.6680 (m-40) REVERT: I 169 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: I 172 ILE cc_start: 0.7908 (mm) cc_final: 0.7611 (mt) REVERT: J 66 ARG cc_start: 0.7251 (mpt180) cc_final: 0.6671 (tpp80) REVERT: J 155 LEU cc_start: 0.8918 (mm) cc_final: 0.8563 (tp) REVERT: K 108 HIS cc_start: 0.7257 (m90) cc_final: 0.7043 (t70) REVERT: K 123 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7593 (pp) REVERT: L 91 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8455 (mmtm) REVERT: L 156 GLN cc_start: 0.8454 (pp30) cc_final: 0.8148 (pp30) outliers start: 41 outliers final: 31 residues processed: 270 average time/residue: 0.1298 time to fit residues: 56.9047 Evaluate side-chains 261 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 153 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 117 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 183 optimal weight: 0.0270 chunk 233 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 overall best weight: 0.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 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 = 0.3936 r_free = 0.3936 target = 0.113222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.080888 restraints weight = 51506.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082250 restraints weight = 32170.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.083508 restraints weight = 22311.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083565 restraints weight = 19178.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.083621 restraints weight = 17307.082| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 21048 Z= 0.118 Angle : 0.625 12.541 28737 Z= 0.297 Chirality : 0.043 0.288 3541 Planarity : 0.003 0.043 3499 Dihedral : 3.981 22.874 2591 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.73 % Allowed : 17.12 % Favored : 81.16 % 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 (0.17), residues: 2441 helix: 1.11 (0.20), residues: 703 sheet: -0.33 (0.24), residues: 473 loop : -1.11 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 131 TYR 0.011 0.001 TYR E 40 PHE 0.031 0.001 PHE C 317 TRP 0.015 0.001 TRP C 112 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (20917) covalent geometry : angle 0.58713 / 0.29 (28380) SS BOND : bond 0.00470 / 0.22 ( 36) SS BOND : angle 1.34712 / 0.83 ( 72) hydrogen bonds : bond 0.03299 / 2.18 ( 720) hydrogen bonds : angle 4.87521 / 3.40 ( 1977) link_ALPHA1-2 : bond 0.00130 / 0.07 ( 4) link_ALPHA1-2 : angle 1.75783 / 1.17 ( 12) link_ALPHA1-3 : bond 0.00638 / 0.32 ( 3) link_ALPHA1-3 : angle 1.81237 / 0.93 ( 9) link_ALPHA1-6 : bond 0.00418 / 0.21 ( 3) link_ALPHA1-6 : angle 1.43203 / 0.97 ( 9) link_BETA1-4 : bond 0.00451 / 0.29 ( 33) link_BETA1-4 : angle 1.69894 / 1.19 ( 99) link_NAG-ASN : bond 0.00451 / 0.24 ( 52) link_NAG-ASN : angle 2.45447 / 1.70 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8711 (p90) cc_final: 0.6547 (m-10) REVERT: A 95 MET cc_start: 0.9143 (ppp) cc_final: 0.8924 (ppp) REVERT: A 446 VAL cc_start: 0.8647 (t) cc_final: 0.8373 (p) REVERT: B 589 ASP cc_start: 0.9258 (t0) cc_final: 0.8618 (t0) REVERT: C 479 TRP cc_start: 0.8315 (m-10) cc_final: 0.7799 (m-90) REVERT: E 92 GLU cc_start: 0.7914 (tp30) cc_final: 0.7707 (tp30) REVERT: G 85 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7920 (mm-30) REVERT: H 62 TRP cc_start: 0.8006 (m-10) cc_final: 0.7759 (m-10) REVERT: H 96 LEU cc_start: 0.8656 (tt) cc_final: 0.8294 (mm) REVERT: I 169 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: I 172 ILE cc_start: 0.8039 (mm) cc_final: 0.7646 (mt) REVERT: J 54 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8347 (pt0) REVERT: J 66 ARG cc_start: 0.7244 (mpt180) cc_final: 0.6614 (tpp80) REVERT: J 155 LEU cc_start: 0.8911 (mm) cc_final: 0.8611 (tp) REVERT: K 108 HIS cc_start: 0.7191 (m90) cc_final: 0.6959 (t70) REVERT: K 123 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7586 (pp) REVERT: L 87 GLU cc_start: 0.8630 (pp20) cc_final: 0.8411 (pp20) REVERT: L 91 LYS cc_start: 0.8715 (mmtm) cc_final: 0.8334 (mmtm) outliers start: 37 outliers final: 26 residues processed: 274 average time/residue: 0.1280 time to fit residues: 57.6231 Evaluate side-chains 263 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 153 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 187 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 204 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 12 optimal weight: 0.0470 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN G 164 ASN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN K 97 ASN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.113747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.081287 restraints weight = 52978.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.083200 restraints weight = 31031.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.084098 restraints weight = 21053.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.084350 restraints weight = 18304.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.084363 restraints weight = 16484.434| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21048 Z= 0.138 Angle : 0.642 12.589 28737 Z= 0.305 Chirality : 0.043 0.291 3541 Planarity : 0.003 0.045 3499 Dihedral : 3.974 24.228 2591 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.24 % Allowed : 17.02 % Favored : 80.74 % 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: -0.39 (0.17), residues: 2441 helix: 1.18 (0.20), residues: 708 sheet: -0.32 (0.24), residues: 479 loop : -1.07 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 131 TYR 0.013 0.001 TYR E 40 PHE 0.032 0.002 PHE C 317 TRP 0.018 0.001 TRP C 112 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (20917) covalent geometry : angle 0.60341 / 0.30 (28380) SS BOND : bond 0.00371 / 0.19 ( 36) SS BOND : angle 1.27030 / 0.80 ( 72) hydrogen bonds : bond 0.03364 / 2.22 ( 720) hydrogen bonds : angle 4.85889 / 3.39 ( 1977) link_ALPHA1-2 : bond 0.00145 / 0.07 ( 4) link_ALPHA1-2 : angle 1.73943 / 1.17 ( 12) link_ALPHA1-3 : bond 0.00600 / 0.30 ( 3) link_ALPHA1-3 : angle 1.84054 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00385 / 0.19 ( 3) link_ALPHA1-6 : angle 1.44572 / 0.97 ( 9) link_BETA1-4 : bond 0.00420 / 0.27 ( 33) link_BETA1-4 : angle 1.69434 / 1.19 ( 99) link_NAG-ASN : bond 0.00447 / 0.24 ( 52) link_NAG-ASN : angle 2.55404 / 1.74 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8741 (p90) cc_final: 0.6538 (m-10) REVERT: A 95 MET cc_start: 0.9142 (ppp) cc_final: 0.8915 (ppp) REVERT: A 446 VAL cc_start: 0.8665 (t) cc_final: 0.8370 (p) REVERT: B 589 ASP cc_start: 0.9285 (t0) cc_final: 0.8641 (t0) REVERT: C 479 TRP cc_start: 0.8291 (m-10) cc_final: 0.7689 (m-90) REVERT: D 648 GLU cc_start: 0.8303 (pp20) cc_final: 0.7988 (pp20) REVERT: E 92 GLU cc_start: 0.7949 (tp30) cc_final: 0.7673 (tp30) REVERT: G 85 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: H 96 LEU cc_start: 0.8754 (tt) cc_final: 0.8391 (mm) REVERT: I 24 ILE cc_start: 0.8500 (pt) cc_final: 0.8270 (mm) REVERT: I 169 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8253 (tm-30) REVERT: J 54 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8372 (pt0) REVERT: J 66 ARG cc_start: 0.7228 (mpt180) cc_final: 0.6643 (tpp80) REVERT: J 155 LEU cc_start: 0.8896 (mm) cc_final: 0.8591 (tp) REVERT: K 108 HIS cc_start: 0.7230 (m90) cc_final: 0.6970 (t70) REVERT: K 123 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7596 (pp) REVERT: L 91 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8367 (mmtm) REVERT: L 156 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8406 (pp30) outliers start: 48 outliers final: 32 residues processed: 276 average time/residue: 0.1353 time to fit residues: 60.6690 Evaluate side-chains 262 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 156 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 169 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN I 52 ASN J 130 ASN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN L 156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.110875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078645 restraints weight = 52309.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079577 restraints weight = 33192.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080848 restraints weight = 23949.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.080805 restraints weight = 20636.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.080933 restraints weight = 18348.272| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21048 Z= 0.184 Angle : 0.688 12.037 28737 Z= 0.330 Chirality : 0.044 0.293 3541 Planarity : 0.004 0.044 3499 Dihedral : 4.124 23.844 2591 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.19 % Allowed : 17.21 % Favored : 80.60 % 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 (0.17), residues: 2441 helix: 1.15 (0.20), residues: 708 sheet: -0.41 (0.24), residues: 478 loop : -1.11 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 131 TYR 0.015 0.002 TYR E 40 PHE 0.025 0.002 PHE H 26 TRP 0.015 0.001 TRP H 28 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (20917) covalent geometry : angle 0.64994 / 0.32 (28380) SS BOND : bond 0.00425 / 0.23 ( 36) SS BOND : angle 1.52717 / 1.05 ( 72) hydrogen bonds : bond 0.03631 / 2.42 ( 720) hydrogen bonds : angle 5.00675 / 3.50 ( 1977) link_ALPHA1-2 : bond 0.00126 / 0.06 ( 4) link_ALPHA1-2 : angle 1.72595 / 1.18 ( 12) link_ALPHA1-3 : bond 0.00527 / 0.26 ( 3) link_ALPHA1-3 : angle 1.89329 / 0.96 ( 9) link_ALPHA1-6 : bond 0.00326 / 0.16 ( 3) link_ALPHA1-6 : angle 1.47833 / 0.99 ( 9) link_BETA1-4 : bond 0.00402 / 0.27 ( 33) link_BETA1-4 : angle 1.72415 / 1.21 ( 99) link_NAG-ASN : bond 0.00474 / 0.26 ( 52) link_NAG-ASN : angle 2.61328 / 1.79 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 0.865 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 61 TYR cc_start: 0.8780 (p90) cc_final: 0.6659 (m-10) REVERT: A 95 MET cc_start: 0.9149 (ppp) cc_final: 0.8916 (ppp) REVERT: A 446 VAL cc_start: 0.8713 (t) cc_final: 0.8432 (p) REVERT: B 530 MET cc_start: 0.8434 (tpp) cc_final: 0.7935 (mtp) REVERT: B 589 ASP cc_start: 0.9282 (t0) cc_final: 0.8544 (t0) REVERT: C 479 TRP cc_start: 0.8371 (m-10) cc_final: 0.7731 (m-90) REVERT: E 92 GLU cc_start: 0.7944 (tp30) cc_final: 0.7668 (tp30) REVERT: F 602 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8119 (mt) REVERT: G 40 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8161 (mt0) REVERT: G 85 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: G 91 GLU cc_start: 0.6780 (tm-30) cc_final: 0.6259 (tm-30) REVERT: H 96 LEU cc_start: 0.8783 (tt) cc_final: 0.8420 (mm) REVERT: I 24 ILE cc_start: 0.8505 (pt) cc_final: 0.8262 (mm) REVERT: I 169 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: J 66 ARG cc_start: 0.7292 (mpt180) cc_final: 0.6680 (tpp80) REVERT: J 155 LEU cc_start: 0.8947 (mm) cc_final: 0.8633 (tp) REVERT: K 108 HIS cc_start: 0.7247 (m90) cc_final: 0.6984 (t70) REVERT: K 123 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7614 (pp) REVERT: L 156 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8247 (pp30) outliers start: 47 outliers final: 36 residues processed: 266 average time/residue: 0.1329 time to fit residues: 58.0714 Evaluate side-chains 262 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain L residue 153 GLU Chi-restraints excluded: chain L residue 156 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 163 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 chunk 238 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN K 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.113356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.081041 restraints weight = 53039.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.082706 restraints weight = 31153.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.083758 restraints weight = 21570.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.083965 restraints weight = 18431.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.084000 restraints weight = 16630.001| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21048 Z= 0.143 Angle : 0.677 12.330 28737 Z= 0.323 Chirality : 0.044 0.355 3541 Planarity : 0.003 0.043 3499 Dihedral : 4.099 24.066 2591 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.96 % Allowed : 17.49 % Favored : 80.55 % 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: -0.44 (0.17), residues: 2441 helix: 1.15 (0.20), residues: 709 sheet: -0.41 (0.23), residues: 488 loop : -1.08 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 131 TYR 0.013 0.001 TYR E 217 PHE 0.030 0.002 PHE H 26 TRP 0.022 0.001 TRP H 157 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (20917) covalent geometry : angle 0.64110 / 0.31 (28380) SS BOND : bond 0.00415 / 0.22 ( 36) SS BOND : angle 1.41877 / 0.96 ( 72) hydrogen bonds : bond 0.03451 / 2.27 ( 720) hydrogen bonds : angle 4.90493 / 3.44 ( 1977) link_ALPHA1-2 : bond 0.00090 / 0.04 ( 4) link_ALPHA1-2 : angle 1.73305 / 1.18 ( 12) link_ALPHA1-3 : bond 0.00594 / 0.30 ( 3) link_ALPHA1-3 : angle 1.82444 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00375 / 0.19 ( 3) link_ALPHA1-6 : angle 1.44205 / 0.97 ( 9) link_BETA1-4 : bond 0.00418 / 0.27 ( 33) link_BETA1-4 : angle 1.67711 / 1.17 ( 99) link_NAG-ASN : bond 0.00459 / 0.25 ( 52) link_NAG-ASN : angle 2.54616 / 1.74 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 0.794 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 61 TYR cc_start: 0.8771 (p90) cc_final: 0.6628 (m-10) REVERT: A 95 MET cc_start: 0.9153 (ppp) cc_final: 0.8924 (ppp) REVERT: A 446 VAL cc_start: 0.8676 (t) cc_final: 0.8400 (p) REVERT: B 530 MET cc_start: 0.8371 (tpp) cc_final: 0.7836 (mtp) REVERT: B 589 ASP cc_start: 0.9287 (t0) cc_final: 0.8551 (t0) REVERT: C 479 TRP cc_start: 0.8321 (m-10) cc_final: 0.7641 (m-90) REVERT: E 92 GLU cc_start: 0.7946 (tp30) cc_final: 0.7665 (tp30) REVERT: F 602 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8154 (mt) REVERT: G 85 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: G 91 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6239 (tm-30) REVERT: H 96 LEU cc_start: 0.8698 (tt) cc_final: 0.8367 (mm) REVERT: I 24 ILE cc_start: 0.8484 (pt) cc_final: 0.8243 (mm) REVERT: I 169 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: J 66 ARG cc_start: 0.7252 (mpt180) cc_final: 0.6658 (tpp80) REVERT: J 155 LEU cc_start: 0.9041 (mm) cc_final: 0.8721 (tp) REVERT: K 108 HIS cc_start: 0.7198 (m90) cc_final: 0.6969 (t70) REVERT: K 123 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7596 (pp) REVERT: L 91 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8257 (mmtm) REVERT: L 156 GLN cc_start: 0.8669 (pp30) cc_final: 0.8408 (pp30) outliers start: 42 outliers final: 35 residues processed: 264 average time/residue: 0.1288 time to fit residues: 55.6309 Evaluate side-chains 261 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 153 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 195 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 198 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 chunk 154 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN D 591 GLN I 52 ASN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.114043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.081728 restraints weight = 52929.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.083320 restraints weight = 31087.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.084305 restraints weight = 21661.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.084586 restraints weight = 18693.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.084662 restraints weight = 16815.094| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21048 Z= 0.127 Angle : 0.667 12.412 28737 Z= 0.318 Chirality : 0.044 0.352 3541 Planarity : 0.003 0.043 3499 Dihedral : 4.041 23.587 2591 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.87 % Allowed : 17.91 % Favored : 80.22 % 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: -0.38 (0.17), residues: 2441 helix: 1.18 (0.20), residues: 709 sheet: -0.40 (0.23), residues: 488 loop : -1.03 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 131 TYR 0.017 0.001 TYR E 217 PHE 0.030 0.001 PHE H 26 TRP 0.023 0.001 TRP H 157 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (20917) covalent geometry : angle 0.63237 / 0.31 (28380) SS BOND : bond 0.00394 / 0.21 ( 36) SS BOND : angle 1.35155 / 0.91 ( 72) hydrogen bonds : bond 0.03351 / 2.19 ( 720) hydrogen bonds : angle 4.85791 / 3.41 ( 1977) link_ALPHA1-2 : bond 0.00122 / 0.06 ( 4) link_ALPHA1-2 : angle 1.74053 / 1.17 ( 12) link_ALPHA1-3 : bond 0.00632 / 0.32 ( 3) link_ALPHA1-3 : angle 1.80187 / 0.93 ( 9) link_ALPHA1-6 : bond 0.00403 / 0.20 ( 3) link_ALPHA1-6 : angle 1.42176 / 0.96 ( 9) link_BETA1-4 : bond 0.00442 / 0.29 ( 33) link_BETA1-4 : angle 1.63427 / 1.14 ( 99) link_NAG-ASN : bond 0.00448 / 0.24 ( 52) link_NAG-ASN : angle 2.46388 / 1.68 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3227.23 seconds wall clock time: 56 minutes 58.66 seconds (3418.66 seconds total)