Starting phenix.real_space_refine on Mon Jul 6 03:02:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tfn_25877/07_2026/7tfn_25877.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfn_25877/07_2026/7tfn_25877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tfn_25877/07_2026/7tfn_25877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfn_25877/07_2026/7tfn_25877.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tfn_25877/07_2026/7tfn_25877.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tfn_25877/07_2026/7tfn_25877.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tfn_25877/07_2026/7tfn_25877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfn_25877/07_2026/7tfn_25877.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16845 atoms to isotropic. 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 104 5.16 5 C 11764 2.51 5 N 3144 2.21 5 O 3680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18692 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3217 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 6 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 6, 'ARG:plan': 7, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3224 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 21, 'TRANS': 400} Chain breaks: 6 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3188 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 388} Chain breaks: 8 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 837 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 843 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 108} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "Q" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 830 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 995 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "Y" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 960 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Z" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 982 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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 Residues with excluded nonbonded symmetry interactions: 45 residue: pdb=" N GLN H 5 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN H 5 " occ=0.00 residue: pdb=" N LEU H 63 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU H 63 " occ=0.00 residue: pdb=" N VAL H 67 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL H 67 " occ=0.00 residue: pdb=" N ASP H 72 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP H 72 " occ=0.00 residue: pdb=" N ASN H 76 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN H 76 " occ=0.00 residue: pdb=" N ALA H 84 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA H 84 " occ=0.00 residue: pdb=" N THR H 110 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR H 110 " occ=0.00 residue: pdb=" N GLN I 5 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN I 5 " occ=0.00 residue: pdb=" N LEU I 63 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU I 63 " occ=0.00 residue: pdb=" N VAL I 67 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL I 67 " occ=0.00 residue: pdb=" N ASP I 72 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP I 72 " occ=0.00 residue: pdb=" N ASN I 76 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN I 76 " occ=0.00 ... (remaining 33 not shown) Time building chain proxies: 3.81, per 1000 atoms: 0.20 Number of scatterers: 18692 At special positions: 0 Unit cell: (126.005, 126.874, 145.123, 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 104 16.00 O 3680 8.00 N 3144 7.00 C 11764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, 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=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " 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 131 " - pdb=" SG CYS C 157 " 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=2.04 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA M 3 " - " MAN M 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 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-ASN " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 448 " " NAG A 604 " - " ASN A 197 " " NAG B 601 " - " ASN B 392 " " NAG B 602 " - " ASN B 197 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 197 " " NAG D 1 " - " ASN A 363 " " NAG E 1 " - " ASN A 276 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 262 " " NAG M 1 " - " ASN B 262 " " NAG N 1 " - " ASN B 448 " " NAG O 1 " - " ASN B 276 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 363 " " NAG T 1 " - " ASN B 386 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 363 " " NAG a 1 " - " ASN C 386 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 276 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 818.0 milliseconds 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 43 sheets defined 22.0% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.554A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 334 through 354 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.732A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 474 through 483 removed outlier: 3.651A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.767A pdb=" N THR B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.029A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 334 through 354 removed outlier: 3.599A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 474 through 481 removed outlier: 4.121A pdb=" N ASN B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.623A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.626A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 480 removed outlier: 3.539A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.654A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.626A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.808A pdb=" N LYS I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.517A pdb=" N ASP I 86 " --> pdb=" O SER I 83 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'J' and resid 26 through 29 removed outlier: 3.625A pdb=" N ARG J 29 " --> pdb=" O SER J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 82 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'P' and resid 61 through 64 removed outlier: 3.503A pdb=" N LYS P 64 " --> pdb=" O PRO P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 64' Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.834A pdb=" N THR P 87 " --> pdb=" O ALA P 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 29 removed outlier: 3.600A pdb=" N ARG Q 29 " --> pdb=" O SER Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'X' and resid 515 through 524 Processing helix chain 'X' and resid 529 through 540 Processing helix chain 'X' and resid 563 through 596 removed outlier: 4.233A pdb=" N LYS X 567 " --> pdb=" O GLN X 563 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP X 596 " --> pdb=" O LEU X 592 " (cutoff:3.500A) Processing helix chain 'X' and resid 618 through 625 removed outlier: 4.280A pdb=" N ILE X 622 " --> pdb=" O ASN X 618 " (cutoff:3.500A) Processing helix chain 'X' and resid 627 through 636 removed outlier: 3.540A pdb=" N TRP X 631 " --> pdb=" O THR X 627 " (cutoff:3.500A) Processing helix chain 'X' and resid 638 through 657 Processing helix chain 'Y' and resid 529 through 536 Processing helix chain 'Y' and resid 536 through 544 removed outlier: 4.564A pdb=" N GLN Y 540 " --> pdb=" O THR Y 536 " (cutoff:3.500A) Processing helix chain 'Y' and resid 562 through 596 removed outlier: 3.568A pdb=" N TRP Y 596 " --> pdb=" O LEU Y 592 " (cutoff:3.500A) Processing helix chain 'Y' and resid 618 through 625 Processing helix chain 'Y' and resid 627 through 636 Processing helix chain 'Y' and resid 638 through 657 Processing helix chain 'Z' and resid 529 through 540 Processing helix chain 'Z' and resid 564 through 596 removed outlier: 3.554A pdb=" N LEU Z 568 " --> pdb=" O HIS Z 564 " (cutoff:3.500A) Processing helix chain 'Z' and resid 618 through 625 removed outlier: 3.812A pdb=" N ASN Z 625 " --> pdb=" O GLU Z 621 " (cutoff:3.500A) Processing helix chain 'Z' and resid 627 through 636 Processing helix chain 'Z' and resid 638 through 660 removed outlier: 4.054A pdb=" N LEU Z 660 " --> pdb=" O ASN Z 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.803A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS A 218 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.758A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 176 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 7.014A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.870A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.958A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.520A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.304A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 307 Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 39 Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.958A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 53 through 56 removed outlier: 4.524A pdb=" N PHE B 53 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS B 218 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.844A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 129 through 130 removed outlier: 4.077A pdb=" N GLU B 190 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 155 through 158 Processing sheet with id=AB8, first strand: chain 'B' and resid 259 through 261 removed outlier: 6.448A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.550A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.461A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 393 through 395 removed outlier: 6.749A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 374 through 378 Processing sheet with id=AC2, first strand: chain 'C' and resid 496 through 499 removed outlier: 5.634A pdb=" N VAL C 36 " --> pdb=" O THR Z 606 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR Z 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC4, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.986A pdb=" N VAL C 120 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA C 433 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 172 through 176 Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AC7, first strand: chain 'C' and resid 376 through 378 removed outlier: 4.035A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN C 332 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.615A pdb=" N TYR H 33 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.822A pdb=" N PHE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.599A pdb=" N TYR I 33 " --> pdb=" O ARG I 95 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.026A pdb=" N PHE I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 9 through 14 removed outlier: 3.677A pdb=" N ALA J 11 " --> pdb=" O ARG J 103 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER J 105 " --> pdb=" O ALA J 11 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE J 33 " --> pdb=" O ARG J 49 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ARG J 49 " --> pdb=" O ILE J 33 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 9 through 14 removed outlier: 3.677A pdb=" N ALA J 11 " --> pdb=" O ARG J 103 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER J 105 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AD9, first strand: chain 'L' and resid 9 through 14 removed outlier: 3.507A pdb=" N SER L 105 " --> pdb=" O ALA L 11 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA L 13 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE L 33 " --> pdb=" O ARG L 49 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AE2, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'P' and resid 11 through 12 removed outlier: 5.173A pdb=" N TYR P 33 " --> pdb=" O ARG P 95 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 11 through 12 removed outlier: 4.041A pdb=" N PHE P 102 " --> pdb=" O ARG P 94 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 5 through 6 Processing sheet with id=AE6, first strand: chain 'Q' and resid 9 through 14 removed outlier: 3.562A pdb=" N SER Q 105 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE Q 33 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG Q 49 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG Q 49 " --> pdb=" O THR Q 53 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 9 through 14 removed outlier: 3.562A pdb=" N SER Q 105 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1866 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: 3.07 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5900 1.34 - 1.46: 4837 1.46 - 1.59: 8200 1.59 - 1.71: 0 1.71 - 1.83: 134 Bond restraints: 19071 Sorted by residual: bond pdb=" N SER A 365 " pdb=" CA SER A 365 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.63e+00 bond pdb=" N ILE C 277 " pdb=" CA ILE C 277 " ideal model delta sigma weight residual 1.463 1.492 -0.029 1.14e-02 7.69e+03 6.63e+00 bond pdb=" N SER C 274 " pdb=" CA SER C 274 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.16e-02 7.43e+03 6.23e+00 bond pdb=" N ILE L 97 " pdb=" CA ILE L 97 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 6.14e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.88e+00 ... (remaining 19066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 25080 1.82 - 3.65: 712 3.65 - 5.47: 128 5.47 - 7.30: 21 7.30 - 9.12: 5 Bond angle restraints: 25946 Sorted by residual: angle pdb=" CA THR L 90 " pdb=" C THR L 90 " pdb=" O THR L 90 " ideal model delta sigma weight residual 121.32 117.20 4.12 1.18e+00 7.18e-01 1.22e+01 angle pdb=" CA ILE C 277 " pdb=" C ILE C 277 " pdb=" O ILE C 277 " ideal model delta sigma weight residual 121.41 118.04 3.37 1.04e+00 9.25e-01 1.05e+01 angle pdb=" CA TRP L 91 " pdb=" C TRP L 91 " pdb=" O TRP L 91 " ideal model delta sigma weight residual 120.63 117.30 3.33 1.05e+00 9.07e-01 1.01e+01 angle pdb=" CB MET C 475 " pdb=" CG MET C 475 " pdb=" SD MET C 475 " ideal model delta sigma weight residual 112.70 121.82 -9.12 3.00e+00 1.11e-01 9.24e+00 angle pdb=" N ASP C 57 " pdb=" CA ASP C 57 " pdb=" C ASP C 57 " ideal model delta sigma weight residual 114.56 110.82 3.74 1.27e+00 6.20e-01 8.68e+00 ... (remaining 25941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 9721 17.64 - 35.29: 920 35.29 - 52.93: 160 52.93 - 70.57: 25 70.57 - 88.21: 13 Dihedral angle restraints: 10839 sinusoidal: 4109 harmonic: 6730 Sorted by residual: dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual -86.00 -149.03 63.03 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " pdb=" SG CYS A 418 " pdb=" CB CYS A 418 " ideal model delta sinusoidal sigma weight residual 93.00 35.39 57.61 1 1.00e+01 1.00e-02 4.46e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -141.72 55.72 1 1.00e+01 1.00e-02 4.19e+01 ... (remaining 10836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.212: 3111 0.212 - 0.424: 21 0.424 - 0.636: 2 0.636 - 0.848: 0 0.848 - 1.060: 2 Chirality restraints: 3136 Sorted by residual: chirality pdb=" C1 MAN D 5 " pdb=" O6 BMA D 3 " pdb=" C2 MAN D 5 " pdb=" O5 MAN D 5 " both_signs ideal model delta sigma weight residual False 2.40 1.80 0.60 2.00e-02 2.50e+03 8.90e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.40e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.33e+02 ... (remaining 3133 not shown) Planarity restraints: 3226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.359 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG G 2 " -0.092 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.327 2.00e-02 2.50e+03 2.75e-01 9.48e+02 pdb=" C7 NAG G 1 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.191 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.476 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.314 2.00e-02 2.50e+03 2.70e-01 9.13e+02 pdb=" C7 NAG F 1 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.012 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.466 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.210 2.00e-02 2.50e+03 ... (remaining 3223 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 195 2.55 - 3.14: 14978 3.14 - 3.73: 28283 3.73 - 4.31: 37652 4.31 - 4.90: 63170 Nonbonded interactions: 144278 Sorted by model distance: nonbonded pdb=" CG2 ILE A 430 " pdb=" O GLY L 94 " model vdw 1.966 3.460 nonbonded pdb=" O GLN Z 563 " pdb=" ND1 HIS Z 564 " model vdw 1.976 3.120 nonbonded pdb=" OE1 GLN J 6 " pdb=" OG1 THR J 102 " model vdw 2.051 3.040 nonbonded pdb=" OG1 THR B 106 " pdb=" OG SER I 54 " model vdw 2.163 3.040 nonbonded pdb=" OG1 THR A 106 " pdb=" OG SER H 54 " model vdw 2.209 3.040 ... (remaining 144273 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' and ((resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 60 or resid 68 through 81 or (resid 82 through 83 and (na \ me N or name CA or name C or name O or name CB )) or resid 84 through 86 or (res \ id 87 and (name N or name CA or name C or name O or name CB )) or resid 88 throu \ gh 90 or (resid 91 through 92 and (name N or name CA or name C or name O or name \ CB )) or resid 93 through 120 or (resid 121 and (name N or name CA or name C or \ name O or name CB )) or resid 122 or (resid 123 and (name N or name CA or name \ C or name O or name CB )) or resid 124 or (resid 128 through 131 and (name N or \ name CA or name C or name O or name CB )) or resid 132 through 135 or (resid 136 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 1 \ 62 or resid 172 through 185 or (resid 189 through 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 202 or (resid 203 through 20 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 205 through \ 210 or (resid 211 and (name N or name CA or name C or name O or name CB )) or re \ sid 212 through 306 or resid 315 through 321 or (resid 321A and (name N or name \ CA or name C or name O or name CB )) or resid 322 through 324 or (resid 325 and \ (name N or name CA or name C or name O or name CB )) or resid 326 through 352 or \ resid 356 through 396 or resid 415 through 459 or resid 466 through 484 or (res \ id 485 and (name N or name CA or name C or name O or name CB )) or resid 486 thr \ ough 503 or resid 603)) selection = (chain 'B' and (resid 34 through 46 or (resid 47 through 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 56 or (resid 57 through \ 60 and (name N or name CA or name C or name O or name CB )) or resid 68 through \ 77 or (resid 78 and (name N or name CA or name C or name O or name CB )) or res \ id 79 through 135 or (resid 136 and (name N or name CA or name C or name O or na \ me CB )) or resid 151 through 230 or (resid 231 through 232 and (name N or name \ CA or name C or name O or name CB )) or resid 233 through 264 or (resid 265 thro \ ugh 269 and (name N or name CA or name C or name O or name CB )) or resid 270 or \ (resid 271 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 2 through 297 or (resid 298 and (name N or name CA or name C or name O or name C \ B )) or resid 299 or (resid 300 through 303 and (name N or name CA or name C or \ name O or name CB )) or resid 304 or (resid 305 through 306 and (name N or name \ CA or name C or name O or name CB )) or (resid 315 through 316 and (name N or na \ me CA or name C or name O or name CB )) or resid 317 through 346 or (resid 347 a \ nd (name N or name CA or name C or name O or name CB )) or resid 348 through 349 \ or (resid 350 through 351 and (name N or name CA or name C or name O or name CB \ )) or resid 352 or (resid 356 through 357 and (name N or name CA or name C or n \ ame O or name CB )) or resid 358 through 396 or resid 415 through 438 or (resid \ 439 through 440 and (name N or name CA or name C or name O or name CB )) or resi \ d 441 or (resid 442 through 444 and (name N or name CA or name C or name O or na \ me CB )) or resid 445 through 459 or (resid 466 and (name N or name CA or name C \ or name O or name CB )) or resid 467 through 484 or (resid 485 and (name N or n \ ame CA or name C or name O or name CB )) or resid 486 through 601)) selection = (chain 'C' and ((resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 46 or (resid 47 through 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 58 or (resid 59 through 60 and (n \ ame N or name CA or name C or name O or name CB )) or resid 68 through 81 or (re \ sid 82 through 83 and (name N or name CA or name C or name O or name CB )) or re \ sid 84 through 86 or (resid 87 and (name N or name CA or name C or name O or nam \ e CB )) or resid 88 through 90 or (resid 91 through 92 and (name N or name CA or \ name C or name O or name CB )) or resid 93 through 120 or (resid 121 and (name \ N or name CA or name C or name O or name CB )) or resid 122 or (resid 123 and (n \ ame N or name CA or name C or name O or name CB )) or resid 124 or (resid 128 th \ rough 131 and (name N or name CA or name C or name O or name CB )) or resid 132 \ through 136 or resid 151 through 162 or resid 172 through 185 or (resid 189 thro \ ugh 190 and (name N or name CA or name C or name O or name CB )) or resid 191 th \ rough 202 or (resid 203 through 204 and (name N or name CA or name C or name O o \ r name CB )) or resid 205 through 206 or (resid 207 and (name N or name CA or na \ me C or name O or name CB )) or resid 208 through 210 or (resid 211 and (name N \ or name CA or name C or name O or name CB )) or resid 212 through 230 or (resid \ 231 through 232 and (name N or name CA or name C or name O or name CB )) or resi \ d 233 through 264 or (resid 265 through 269 and (name N or name CA or name C or \ name O or name CB )) or resid 270 or (resid 271 and (name N or name CA or name C \ or name O or name CB )) or resid 272 through 297 or (resid 298 and (name N or n \ ame CA or name C or name O or name CB )) or resid 299 or (resid 300 through 303 \ and (name N or name CA or name C or name O or name CB )) or resid 304 or (resid \ 305 through 306 and (name N or name CA or name C or name O or name CB )) or (res \ id 315 through 316 and (name N or name CA or name C or name O or name CB )) or r \ esid 317 through 321 or (resid 321A and (name N or name CA or name C or name O o \ r name CB )) or resid 322 through 324 or (resid 325 and (name N or name CA or na \ me C or name O or name CB )) or resid 326 through 346 or (resid 347 and (name N \ or name CA or name C or name O or name CB )) or resid 348 through 349 or (resid \ 350 through 351 and (name N or name CA or name C or name O or name CB )) or resi \ d 352 or (resid 356 through 357 and (name N or name CA or name C or name O or na \ me CB )) or resid 358 through 438 or (resid 439 through 440 and (name N or name \ CA or name C or name O or name CB )) or resid 441 or (resid 442 through 444 and \ (name N or name CA or name C or name O or name CB )) or resid 445 through 459 or \ (resid 466 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 7 through 499 or (resid 500 through 503 and (name N or name CA or name C or name \ O or name CB )) or resid 603)) } ncs_group { reference = chain 'E' selection = chain 'O' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'F' selection = chain 'N' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'a' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = (chain 'H' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 113)) selection = (chain 'I' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 113)) selection = chain 'P' } ncs_group { reference = (chain 'J' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 107)) selection = (chain 'L' and (resid 2 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 107)) selection = (chain 'Q' and resid 2 through 107) } ncs_group { reference = (chain 'X' and (resid 522 through 534 or (resid 535 through 536 and (name N or n \ ame CA or name C or name O or name CB )) or resid 537 through 539 or (resid 540 \ and (name N or name CA or name C or name O or name CB )) or resid 560 through 57 \ 0 or (resid 571 and (name N or name CA or name C or name O or name CB )) or resi \ d 572 through 647 or (resid 648 and (name N or name CA or name C or name O or na \ me CB )) or resid 649 through 657)) selection = (chain 'Y' and (resid 522 through 537 or (resid 538 through 540 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 560 through 562 and (name N o \ r name CA or name C or name O or name CB )) or resid 563 or (resid 564 and (name \ N or name CA or name C or name O or name CB )) or resid 565 through 587 or (res \ id 588 and (name N or name CA or name C or name O or name CB )) or resid 589 thr \ ough 594 or (resid 595 and (name N or name CA or name C or name O or name CB )) \ or resid 596 through 615 or (resid 616 and (name N or name CA or name C or name \ O or name CB )) or resid 617 through 647 or (resid 648 and (name N or name CA or \ name C or name O or name CB )) or resid 649 through 654 or (resid 655 and (name \ N or name CA or name C or name O or name CB )) or resid 656 or (resid 657 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'Z' and (resid 522 through 535 or (resid 536 and (name N or name CA or na \ me C or name O or name CB )) or resid 537 or (resid 538 through 540 and (name N \ or name CA or name C or name O or name CB )) or (resid 560 through 562 and (name \ N or name CA or name C or name O or name CB )) or resid 563 or (resid 564 and ( \ name N or name CA or name C or name O or name CB )) or resid 565 through 566 or \ (resid 567 and (name N or name CA or name C or name O or name CB )) or resid 568 \ through 570 or (resid 571 and (name N or name CA or name C or name O or name CB \ )) or resid 572 through 587 or (resid 588 and (name N or name CA or name C or n \ ame O or name CB )) or resid 589 through 594 or (resid 595 and (name N or name C \ A or name C or name O or name CB )) or resid 596 through 615 or (resid 616 and ( \ name N or name CA or name C or name O or name CB )) or resid 617 through 654 or \ (resid 655 and (name N or name CA or name C or name O or name CB )) or resid 656 \ or (resid 657 and (name N or name CA or name C or name O or name CB )))) } 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=0.00 max=1.00 mean=0.97 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: 6.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.360 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.004 0.049 19158 Z= 0.209 Angle : 0.772 11.997 26176 Z= 0.364 Chirality : 0.060 1.060 3136 Planarity : 0.012 0.305 3203 Dihedral : 13.805 88.214 6402 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.94 % Favored : 93.89 % Rotamer: Outliers : 0.10 % Allowed : 0.42 % Favored : 99.48 % 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: -0.97 (0.18), residues: 2274 helix: 1.44 (0.26), residues: 439 sheet: -0.70 (0.20), residues: 652 loop : -1.42 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 95 TYR 0.014 0.001 TYR B 217 PHE 0.016 0.001 PHE C 53 TRP 0.021 0.001 TRP C 45 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 (19071) covalent geometry : angle 0.71793 / 0.35 (25946) SS BOND : bond 0.00342 / 0.26 ( 31) SS BOND : angle 0.95426 / 0.62 ( 62) hydrogen bonds : bond 0.12234 / 8.27 ( 682) hydrogen bonds : angle 5.81540 / 4.04 ( 1866) link_ALPHA1-3 : bond 0.00609 / 0.32 ( 5) link_ALPHA1-3 : angle 1.60189 / 0.81 ( 15) link_ALPHA1-6 : bond 0.01440 / 0.76 ( 2) link_ALPHA1-6 : angle 5.01842 / 1.97 ( 6) link_BETA1-4 : bond 0.00601 / 0.38 ( 26) link_BETA1-4 : angle 2.71443 / 1.78 ( 78) link_NAG-ASN : bond 0.00803 / 0.47 ( 23) link_NAG-ASN : angle 4.50689 / 2.84 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 251 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.4760 (p-90) cc_final: 0.4523 (p-90) REVERT: H 11 LEU cc_start: 0.8533 (mt) cc_final: 0.8266 (mt) REVERT: I 4 LEU cc_start: 0.8474 (mm) cc_final: 0.8086 (mm) REVERT: J 52 VAL cc_start: 0.9080 (m) cc_final: 0.8684 (p) REVERT: L 49 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6146 (mtt180) REVERT: L 51 ASP cc_start: 0.6896 (p0) cc_final: 0.6626 (p0) REVERT: L 70 GLU cc_start: 0.4861 (pp20) cc_final: 0.4622 (pp20) outliers start: 2 outliers final: 0 residues processed: 252 average time/residue: 0.1126 time to fit residues: 44.8983 Evaluate side-chains 175 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.0470 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 0.0370 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS B 66 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 591 GLN ** Y 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.082280 restraints weight = 46146.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.082657 restraints weight = 40436.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.083244 restraints weight = 35774.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083661 restraints weight = 30510.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.083766 restraints weight = 28313.504| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19158 Z= 0.149 Angle : 0.682 15.130 26176 Z= 0.326 Chirality : 0.047 0.424 3136 Planarity : 0.004 0.047 3203 Dihedral : 4.586 36.936 2484 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.07 % Favored : 93.80 % Rotamer: Outliers : 0.78 % Allowed : 9.92 % Favored : 89.30 % 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: -0.92 (0.18), residues: 2274 helix: 1.42 (0.25), residues: 447 sheet: -0.65 (0.20), residues: 655 loop : -1.40 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 617 TYR 0.014 0.001 TYR I 33 PHE 0.030 0.001 PHE B 376 TRP 0.025 0.001 TRP B 479 HIS 0.007 0.001 HIS Z 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (19071) covalent geometry : angle 0.64253 / 0.32 (25946) SS BOND : bond 0.00563 / 0.27 ( 31) SS BOND : angle 1.08220 / 0.72 ( 62) hydrogen bonds : bond 0.03804 / 2.53 ( 682) hydrogen bonds : angle 5.13533 / 3.54 ( 1866) link_ALPHA1-3 : bond 0.00497 / 0.26 ( 5) link_ALPHA1-3 : angle 1.59905 / 0.80 ( 15) link_ALPHA1-6 : bond 0.01793 / 0.94 ( 2) link_ALPHA1-6 : angle 2.40922 / 1.07 ( 6) link_BETA1-4 : bond 0.00563 / 0.34 ( 26) link_BETA1-4 : angle 2.07697 / 1.36 ( 78) link_NAG-ASN : bond 0.00523 / 0.30 ( 23) link_NAG-ASN : angle 3.78605 / 2.32 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8200 (mmm) cc_final: 0.7635 (mmt) REVERT: B 424 ILE cc_start: 0.7669 (mm) cc_final: 0.7408 (mm) REVERT: J 52 VAL cc_start: 0.8992 (m) cc_final: 0.8542 (p) REVERT: Y 534 SER cc_start: 0.8937 (p) cc_final: 0.8728 (t) outliers start: 15 outliers final: 11 residues processed: 206 average time/residue: 0.1241 time to fit residues: 41.3571 Evaluate side-chains 186 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain X residue 641 ILE Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 622 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 151 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 162 optimal weight: 0.6980 chunk 229 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 chunk 178 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN B 289 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN C 478 ASN J 77 ASN X 591 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.079871 restraints weight = 47043.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.080146 restraints weight = 42100.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080650 restraints weight = 37323.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.081018 restraints weight = 32836.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.081107 restraints weight = 30871.798| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19158 Z= 0.191 Angle : 0.668 14.841 26176 Z= 0.323 Chirality : 0.046 0.418 3136 Planarity : 0.004 0.049 3203 Dihedral : 4.523 20.305 2480 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.64 % Favored : 93.27 % Rotamer: Outliers : 1.87 % Allowed : 13.40 % Favored : 84.74 % 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: -0.89 (0.18), residues: 2274 helix: 1.45 (0.25), residues: 441 sheet: -0.61 (0.20), residues: 658 loop : -1.39 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 95 TYR 0.019 0.002 TYR Z 638 PHE 0.025 0.002 PHE B 376 TRP 0.026 0.002 TRP B 479 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (19071) covalent geometry : angle 0.63273 / 0.31 (25946) SS BOND : bond 0.00435 / 0.24 ( 31) SS BOND : angle 1.16300 / 0.77 ( 62) hydrogen bonds : bond 0.03731 / 2.47 ( 682) hydrogen bonds : angle 5.06138 / 3.47 ( 1866) link_ALPHA1-3 : bond 0.00500 / 0.26 ( 5) link_ALPHA1-3 : angle 1.50993 / 0.78 ( 15) link_ALPHA1-6 : bond 0.01346 / 0.70 ( 2) link_ALPHA1-6 : angle 2.19531 / 0.96 ( 6) link_BETA1-4 : bond 0.00512 / 0.32 ( 26) link_BETA1-4 : angle 1.97260 / 1.25 ( 78) link_NAG-ASN : bond 0.00463 / 0.29 ( 23) link_NAG-ASN : angle 3.51828 / 2.18 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8344 (mmm) cc_final: 0.7839 (mmt) REVERT: J 61 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7502 (mtm180) REVERT: L 36 TYR cc_start: 0.8754 (m-80) cc_final: 0.8517 (m-80) outliers start: 36 outliers final: 22 residues processed: 210 average time/residue: 0.1234 time to fit residues: 42.2559 Evaluate side-chains 186 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 608 VAL Chi-restraints excluded: chain X residue 632 ASP Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 622 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 155 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN J 6 GLN J 42 GLN L 39 GLN Y 650 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.099876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077619 restraints weight = 47657.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.076472 restraints weight = 49823.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077177 restraints weight = 49238.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077569 restraints weight = 39807.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077760 restraints weight = 37078.290| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 19158 Z= 0.307 Angle : 0.761 15.029 26176 Z= 0.372 Chirality : 0.048 0.409 3136 Planarity : 0.004 0.057 3203 Dihedral : 4.927 20.817 2480 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.65 % Favored : 92.22 % Rotamer: Outliers : 3.43 % Allowed : 15.73 % Favored : 80.84 % 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: -1.19 (0.18), residues: 2274 helix: 1.14 (0.25), residues: 443 sheet: -0.80 (0.21), residues: 638 loop : -1.55 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 95 TYR 0.023 0.002 TYR Z 638 PHE 0.022 0.002 PHE B 376 TRP 0.023 0.002 TRP C 479 HIS 0.008 0.001 HIS I 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.31 (19071) covalent geometry : angle 0.72755 / 0.36 (25946) SS BOND : bond 0.00495 / 0.28 ( 31) SS BOND : angle 1.25110 / 0.86 ( 62) hydrogen bonds : bond 0.04193 / 2.77 ( 682) hydrogen bonds : angle 5.33033 / 3.65 ( 1866) link_ALPHA1-3 : bond 0.00380 / 0.19 ( 5) link_ALPHA1-3 : angle 1.62391 / 0.84 ( 15) link_ALPHA1-6 : bond 0.01421 / 0.75 ( 2) link_ALPHA1-6 : angle 2.09797 / 0.90 ( 6) link_BETA1-4 : bond 0.00513 / 0.33 ( 26) link_BETA1-4 : angle 2.03865 / 1.27 ( 78) link_NAG-ASN : bond 0.00624 / 0.41 ( 23) link_NAG-ASN : angle 3.72484 / 2.35 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 171 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8461 (t0) cc_final: 0.8085 (t0) REVERT: A 475 MET cc_start: 0.8388 (mmm) cc_final: 0.7956 (mmt) REVERT: H 33 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7075 (m-80) REVERT: I 98 ASP cc_start: 0.8682 (p0) cc_final: 0.8199 (p0) REVERT: Q 36 TYR cc_start: 0.9129 (m-80) cc_final: 0.8887 (m-80) outliers start: 66 outliers final: 39 residues processed: 221 average time/residue: 0.1088 time to fit residues: 39.4908 Evaluate side-chains 191 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain X residue 529 THR Chi-restraints excluded: chain X residue 537 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 608 VAL Chi-restraints excluded: chain X residue 632 ASP Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Z residue 570 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 38 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 0.0010 chunk 214 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 229 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 GLN X 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.103012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080657 restraints weight = 46752.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.081115 restraints weight = 44394.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.081519 restraints weight = 41356.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.081855 restraints weight = 35038.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.081912 restraints weight = 32991.977| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19158 Z= 0.133 Angle : 0.660 14.575 26176 Z= 0.320 Chirality : 0.046 0.444 3136 Planarity : 0.003 0.050 3203 Dihedral : 4.583 21.467 2480 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.98 % Rotamer: Outliers : 2.44 % Allowed : 18.43 % Favored : 79.13 % 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: -0.91 (0.18), residues: 2274 helix: 1.46 (0.25), residues: 448 sheet: -0.65 (0.21), residues: 661 loop : -1.40 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 419 TYR 0.015 0.001 TYR Z 638 PHE 0.022 0.001 PHE B 376 TRP 0.016 0.001 TRP C 45 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (19071) covalent geometry : angle 0.62730 / 0.31 (25946) SS BOND : bond 0.00464 / 0.28 ( 31) SS BOND : angle 1.13875 / 0.78 ( 62) hydrogen bonds : bond 0.03576 / 2.34 ( 682) hydrogen bonds : angle 5.03124 / 3.47 ( 1866) link_ALPHA1-3 : bond 0.00576 / 0.30 ( 5) link_ALPHA1-3 : angle 1.46020 / 0.76 ( 15) link_ALPHA1-6 : bond 0.01438 / 0.75 ( 2) link_ALPHA1-6 : angle 2.13452 / 0.93 ( 6) link_BETA1-4 : bond 0.00555 / 0.36 ( 26) link_BETA1-4 : angle 1.87572 / 1.17 ( 78) link_NAG-ASN : bond 0.00430 / 0.26 ( 23) link_NAG-ASN : angle 3.38135 / 2.11 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8420 (mtp) cc_final: 0.8200 (mtm) REVERT: A 457 ASP cc_start: 0.8413 (t0) cc_final: 0.8102 (t0) REVERT: C 368 ASP cc_start: 0.7048 (p0) cc_final: 0.6698 (p0) REVERT: H 33 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.6925 (m-80) REVERT: L 36 TYR cc_start: 0.8737 (m-80) cc_final: 0.8449 (m-80) REVERT: Z 619 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8517 (tt) outliers start: 47 outliers final: 26 residues processed: 220 average time/residue: 0.1157 time to fit residues: 41.5647 Evaluate side-chains 194 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain X residue 529 THR Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 641 ILE Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Z residue 619 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 174 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 591 GLN Z 637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.100174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077323 restraints weight = 47299.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077202 restraints weight = 42280.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.077568 restraints weight = 39580.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078081 restraints weight = 33662.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.078230 restraints weight = 30736.993| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19158 Z= 0.280 Angle : 0.742 14.844 26176 Z= 0.361 Chirality : 0.048 0.405 3136 Planarity : 0.004 0.054 3203 Dihedral : 4.801 23.655 2480 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.74 % Favored : 92.17 % Rotamer: Outliers : 3.01 % Allowed : 19.37 % Favored : 77.62 % 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: -1.08 (0.18), residues: 2274 helix: 1.30 (0.25), residues: 443 sheet: -0.75 (0.21), residues: 644 loop : -1.50 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 95 TYR 0.017 0.002 TYR Z 638 PHE 0.018 0.002 PHE J 87 TRP 0.019 0.002 TRP C 479 HIS 0.006 0.001 HIS I 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.28 (19071) covalent geometry : angle 0.70945 / 0.35 (25946) SS BOND : bond 0.00567 / 0.29 ( 31) SS BOND : angle 1.33660 / 0.90 ( 62) hydrogen bonds : bond 0.03964 / 2.61 ( 682) hydrogen bonds : angle 5.21334 / 3.58 ( 1866) link_ALPHA1-3 : bond 0.00400 / 0.21 ( 5) link_ALPHA1-3 : angle 1.60346 / 0.83 ( 15) link_ALPHA1-6 : bond 0.01443 / 0.76 ( 2) link_ALPHA1-6 : angle 2.07692 / 0.89 ( 6) link_BETA1-4 : bond 0.00517 / 0.34 ( 26) link_BETA1-4 : angle 1.97558 / 1.22 ( 78) link_NAG-ASN : bond 0.00562 / 0.36 ( 23) link_NAG-ASN : angle 3.57740 / 2.27 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8496 (t0) cc_final: 0.8185 (t0) REVERT: H 33 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.6924 (m-80) REVERT: J 61 ARG cc_start: 0.7740 (mtm180) cc_final: 0.7529 (ptm-80) REVERT: L 95 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8771 (tt) REVERT: X 530 MET cc_start: 0.8252 (tpp) cc_final: 0.7790 (mmt) outliers start: 58 outliers final: 45 residues processed: 207 average time/residue: 0.1202 time to fit residues: 40.7541 Evaluate side-chains 202 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain X residue 529 THR Chi-restraints excluded: chain X residue 537 LEU Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 608 VAL Chi-restraints excluded: chain X residue 641 ILE Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 635 ILE Chi-restraints excluded: chain Z residue 626 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 212 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 225 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 591 GLN ** Z 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079713 restraints weight = 46698.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.080766 restraints weight = 38715.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081407 restraints weight = 32448.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.081611 restraints weight = 30241.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.081688 restraints weight = 29176.069| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19158 Z= 0.132 Angle : 0.663 14.504 26176 Z= 0.320 Chirality : 0.046 0.431 3136 Planarity : 0.003 0.049 3203 Dihedral : 4.516 23.764 2480 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 2.34 % Allowed : 20.92 % Favored : 76.74 % 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: -0.84 (0.18), residues: 2274 helix: 1.55 (0.25), residues: 449 sheet: -0.54 (0.21), residues: 647 loop : -1.42 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 617 TYR 0.014 0.001 TYR Z 638 PHE 0.018 0.001 PHE B 376 TRP 0.015 0.001 TRP B 479 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (19071) covalent geometry : angle 0.63183 / 0.31 (25946) SS BOND : bond 0.00506 / 0.29 ( 31) SS BOND : angle 1.14271 / 0.74 ( 62) hydrogen bonds : bond 0.03484 / 2.27 ( 682) hydrogen bonds : angle 4.94093 / 3.41 ( 1866) link_ALPHA1-3 : bond 0.00570 / 0.30 ( 5) link_ALPHA1-3 : angle 1.48041 / 0.78 ( 15) link_ALPHA1-6 : bond 0.01367 / 0.72 ( 2) link_ALPHA1-6 : angle 2.07834 / 0.90 ( 6) link_BETA1-4 : bond 0.00541 / 0.35 ( 26) link_BETA1-4 : angle 1.83120 / 1.14 ( 78) link_NAG-ASN : bond 0.00416 / 0.25 ( 23) link_NAG-ASN : angle 3.32034 / 2.08 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 179 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8414 (mtp) cc_final: 0.8196 (mtm) REVERT: A 457 ASP cc_start: 0.8390 (t0) cc_final: 0.8170 (t0) REVERT: C 368 ASP cc_start: 0.6956 (p0) cc_final: 0.6662 (p0) REVERT: H 33 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7005 (m-10) REVERT: L 36 TYR cc_start: 0.8716 (m-80) cc_final: 0.8431 (m-80) REVERT: P 96 ASP cc_start: 0.8666 (t0) cc_final: 0.8388 (t70) REVERT: Q 31 TYR cc_start: 0.8221 (m-80) cc_final: 0.8000 (m-10) outliers start: 45 outliers final: 34 residues processed: 214 average time/residue: 0.1248 time to fit residues: 43.7581 Evaluate side-chains 205 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain X residue 641 ILE Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 635 ILE Chi-restraints excluded: chain Z residue 629 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 204 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 45 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 591 GLN ** Z 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.101653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.079691 restraints weight = 47152.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.079469 restraints weight = 42129.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.080125 restraints weight = 41974.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.080411 restraints weight = 34274.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.080436 restraints weight = 33354.564| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19158 Z= 0.199 Angle : 0.687 14.508 26176 Z= 0.332 Chirality : 0.046 0.406 3136 Planarity : 0.004 0.050 3203 Dihedral : 4.543 21.678 2480 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.17 % Favored : 92.74 % Rotamer: Outliers : 2.91 % Allowed : 20.51 % Favored : 76.58 % 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: -0.87 (0.18), residues: 2274 helix: 1.51 (0.25), residues: 449 sheet: -0.61 (0.21), residues: 648 loop : -1.39 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 617 TYR 0.014 0.002 TYR Q 31 PHE 0.017 0.002 PHE B 376 TRP 0.032 0.001 TRP A 69 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (19071) covalent geometry : angle 0.65514 / 0.33 (25946) SS BOND : bond 0.00496 / 0.29 ( 31) SS BOND : angle 1.15236 / 0.75 ( 62) hydrogen bonds : bond 0.03617 / 2.38 ( 682) hydrogen bonds : angle 4.99577 / 3.44 ( 1866) link_ALPHA1-3 : bond 0.00470 / 0.24 ( 5) link_ALPHA1-3 : angle 1.55428 / 0.81 ( 15) link_ALPHA1-6 : bond 0.01441 / 0.76 ( 2) link_ALPHA1-6 : angle 2.04032 / 0.88 ( 6) link_BETA1-4 : bond 0.00511 / 0.33 ( 26) link_BETA1-4 : angle 1.87195 / 1.16 ( 78) link_NAG-ASN : bond 0.00452 / 0.28 ( 23) link_NAG-ASN : angle 3.38321 / 2.13 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8484 (t0) cc_final: 0.8188 (t0) REVERT: B 448 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8178 (p0) REVERT: H 33 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: I 50 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7702 (p-80) outliers start: 56 outliers final: 44 residues processed: 219 average time/residue: 0.1156 time to fit residues: 41.5902 Evaluate side-chains 212 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 50 HIS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain X residue 529 THR Chi-restraints excluded: chain X residue 537 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 635 ILE Chi-restraints excluded: chain Z residue 629 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 77 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 182 optimal weight: 0.0030 chunk 62 optimal weight: 7.9990 chunk 223 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 10 optimal weight: 0.0170 chunk 61 optimal weight: 3.9990 overall best weight: 0.7030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.080571 restraints weight = 46568.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081082 restraints weight = 39777.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.081308 restraints weight = 35794.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.081820 restraints weight = 31867.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081855 restraints weight = 30619.564| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19158 Z= 0.128 Angle : 0.662 14.654 26176 Z= 0.319 Chirality : 0.045 0.417 3136 Planarity : 0.003 0.049 3203 Dihedral : 4.373 22.751 2480 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 2.65 % Allowed : 21.39 % Favored : 75.96 % 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: -0.73 (0.18), residues: 2274 helix: 1.68 (0.25), residues: 449 sheet: -0.43 (0.21), residues: 639 loop : -1.39 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 40 TYR 0.017 0.001 TYR C 484 PHE 0.017 0.001 PHE B 376 TRP 0.031 0.001 TRP A 69 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (19071) covalent geometry : angle 0.63155 / 0.31 (25946) SS BOND : bond 0.00440 / 0.27 ( 31) SS BOND : angle 1.07556 / 0.69 ( 62) hydrogen bonds : bond 0.03347 / 2.19 ( 682) hydrogen bonds : angle 4.84320 / 3.35 ( 1866) link_ALPHA1-3 : bond 0.00576 / 0.30 ( 5) link_ALPHA1-3 : angle 1.49228 / 0.79 ( 15) link_ALPHA1-6 : bond 0.01347 / 0.71 ( 2) link_ALPHA1-6 : angle 2.02043 / 0.88 ( 6) link_BETA1-4 : bond 0.00552 / 0.36 ( 26) link_BETA1-4 : angle 1.79787 / 1.13 ( 78) link_NAG-ASN : bond 0.00421 / 0.25 ( 23) link_NAG-ASN : angle 3.28335 / 2.06 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7937 (tp) REVERT: A 256 SER cc_start: 0.9014 (p) cc_final: 0.8798 (p) REVERT: A 457 ASP cc_start: 0.8414 (t0) cc_final: 0.8173 (t0) REVERT: C 179 LEU cc_start: 0.9112 (pt) cc_final: 0.8403 (mt) REVERT: C 484 TYR cc_start: 0.8588 (p90) cc_final: 0.8316 (p90) REVERT: H 33 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.6937 (m-80) REVERT: I 50 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7585 (p-80) REVERT: L 36 TYR cc_start: 0.8681 (m-80) cc_final: 0.8458 (m-80) outliers start: 51 outliers final: 39 residues processed: 224 average time/residue: 0.1183 time to fit residues: 43.5911 Evaluate side-chains 215 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 50 HIS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain X residue 537 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 635 ILE Chi-restraints excluded: chain Z residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 184 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.103419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.079895 restraints weight = 46560.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081201 restraints weight = 41318.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.081825 restraints weight = 32645.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082100 restraints weight = 29061.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.082198 restraints weight = 28197.420| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19158 Z= 0.138 Angle : 0.662 14.434 26176 Z= 0.320 Chirality : 0.046 0.403 3136 Planarity : 0.003 0.049 3203 Dihedral : 4.326 21.676 2480 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.46 % Favored : 93.45 % Rotamer: Outliers : 2.44 % Allowed : 21.34 % Favored : 76.22 % 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: -0.70 (0.18), residues: 2274 helix: 1.70 (0.25), residues: 449 sheet: -0.43 (0.21), residues: 643 loop : -1.36 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 29 TYR 0.019 0.001 TYR C 484 PHE 0.017 0.001 PHE B 376 TRP 0.037 0.001 TRP B 479 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (19071) covalent geometry : angle 0.63136 / 0.31 (25946) SS BOND : bond 0.00471 / 0.28 ( 31) SS BOND : angle 1.10599 / 0.71 ( 62) hydrogen bonds : bond 0.03358 / 2.20 ( 682) hydrogen bonds : angle 4.83216 / 3.33 ( 1866) link_ALPHA1-3 : bond 0.00550 / 0.29 ( 5) link_ALPHA1-3 : angle 1.50671 / 0.79 ( 15) link_ALPHA1-6 : bond 0.01308 / 0.69 ( 2) link_ALPHA1-6 : angle 1.97509 / 0.86 ( 6) link_BETA1-4 : bond 0.00542 / 0.35 ( 26) link_BETA1-4 : angle 1.79798 / 1.12 ( 78) link_NAG-ASN : bond 0.00397 / 0.24 ( 23) link_NAG-ASN : angle 3.25420 / 2.04 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7951 (tp) REVERT: A 256 SER cc_start: 0.9012 (p) cc_final: 0.8809 (p) REVERT: A 457 ASP cc_start: 0.8434 (t0) cc_final: 0.8179 (t0) REVERT: B 448 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8155 (p0) REVERT: C 179 LEU cc_start: 0.9063 (pt) cc_final: 0.8282 (mt) REVERT: H 33 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7025 (m-10) REVERT: I 50 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7571 (p-80) REVERT: L 36 TYR cc_start: 0.8686 (m-80) cc_final: 0.8463 (m-80) REVERT: Y 648 GLU cc_start: 0.8300 (tp30) cc_final: 0.8058 (tp30) outliers start: 47 outliers final: 39 residues processed: 213 average time/residue: 0.1114 time to fit residues: 39.5375 Evaluate side-chains 217 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 50 HIS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain X residue 537 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 584 GLU Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 635 ILE Chi-restraints excluded: chain Z residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 57 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 182 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080453 restraints weight = 46633.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081747 restraints weight = 41177.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082100 restraints weight = 33048.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.082453 restraints weight = 30259.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.082564 restraints weight = 28850.973| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19158 Z= 0.133 Angle : 0.657 14.431 26176 Z= 0.317 Chirality : 0.045 0.398 3136 Planarity : 0.003 0.049 3203 Dihedral : 4.258 21.479 2480 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 2.54 % Allowed : 21.50 % Favored : 75.96 % 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: -0.67 (0.18), residues: 2274 helix: 1.75 (0.25), residues: 452 sheet: -0.39 (0.21), residues: 641 loop : -1.37 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 40 TYR 0.012 0.001 TYR Q 36 PHE 0.017 0.001 PHE B 376 TRP 0.025 0.001 TRP A 69 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (19071) covalent geometry : angle 0.62714 / 0.31 (25946) SS BOND : bond 0.00436 / 0.26 ( 31) SS BOND : angle 1.08633 / 0.69 ( 62) hydrogen bonds : bond 0.03282 / 2.15 ( 682) hydrogen bonds : angle 4.77572 / 3.30 ( 1866) link_ALPHA1-3 : bond 0.00557 / 0.29 ( 5) link_ALPHA1-3 : angle 1.50838 / 0.79 ( 15) link_ALPHA1-6 : bond 0.01314 / 0.69 ( 2) link_ALPHA1-6 : angle 1.93918 / 0.84 ( 6) link_BETA1-4 : bond 0.00541 / 0.35 ( 26) link_BETA1-4 : angle 1.77760 / 1.11 ( 78) link_NAG-ASN : bond 0.00396 / 0.24 ( 23) link_NAG-ASN : angle 3.21909 / 2.02 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2477.31 seconds wall clock time: 44 minutes 2.18 seconds (2642.18 seconds total)