Starting phenix.real_space_refine on Fri Jun 27 22:20:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tfn_25877/06_2025/7tfn_25877.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfn_25877/06_2025/7tfn_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_25877/06_2025/7tfn_25877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfn_25877/06_2025/7tfn_25877.map" model { file = "/net/cci-nas-00/data/ceres_data/7tfn_25877/06_2025/7tfn_25877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfn_25877/06_2025/7tfn_25877.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 6, 'ARG:plan': 7, 'ASP:plan': 3} 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: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 3} 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: {'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'ARG:plan': 1, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 2, 'ARG:plan': 1} 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 9 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: 11.05, per 1000 atoms: 0.59 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: 5.60 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.58 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: 7.19 Time building geometry restraints manager: 6.20 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 - 24.49: 11164 24.49 - 48.98: 647 48.98 - 73.47: 90 73.47 - 97.95: 74 97.95 - 122.44: 46 Dihedral angle restraints: 12021 sinusoidal: 5291 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 12018 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 503 or resid 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: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 46.140 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.110 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 18.093 122.442 7584 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (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 TRP 0.021 0.001 TRP C 45 HIS 0.006 0.001 HIS A 72 PHE 0.016 0.001 PHE C 53 TYR 0.014 0.001 TYR B 217 ARG 0.009 0.000 ARG I 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00803 ( 23) link_NAG-ASN : angle 4.50689 ( 69) link_ALPHA1-6 : bond 0.01440 ( 2) link_ALPHA1-6 : angle 5.01842 ( 6) link_BETA1-4 : bond 0.00601 ( 26) link_BETA1-4 : angle 2.71443 ( 78) link_ALPHA1-3 : bond 0.00609 ( 5) link_ALPHA1-3 : angle 1.60189 ( 15) hydrogen bonds : bond 0.12234 ( 682) hydrogen bonds : angle 5.81540 ( 1866) SS BOND : bond 0.00342 ( 31) SS BOND : angle 0.95426 ( 62) covalent geometry : bond 0.00415 (19071) covalent geometry : angle 0.71793 (25946) *********************** 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 : 1.994 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: 0.4620 (pp20) outliers start: 2 outliers final: 0 residues processed: 252 average time/residue: 0.2854 time to fit residues: 112.6547 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 : 2.086 ------------------------------------------------------------------------------- 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 195 optimal weight: 0.0870 chunk 175 optimal weight: 6.9990 chunk 97 optimal weight: 0.0470 chunk 59 optimal weight: 0.9980 chunk 118 optimal weight: 0.0170 chunk 93 optimal weight: 8.9990 chunk 181 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 66 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN X 591 GLN ** Y 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082973 restraints weight = 45999.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.083811 restraints weight = 37366.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.084711 restraints weight = 31255.535| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19158 Z= 0.124 Angle : 0.698 15.163 26176 Z= 0.326 Chirality : 0.048 0.449 3136 Planarity : 0.004 0.047 3203 Dihedral : 14.222 115.841 3666 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.85 % Favored : 94.02 % Rotamer: Outliers : 0.57 % Allowed : 10.28 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2274 helix: 1.48 (0.25), residues: 447 sheet: -0.59 (0.20), residues: 653 loop : -1.38 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 479 HIS 0.006 0.001 HIS Z 564 PHE 0.029 0.001 PHE B 376 TYR 0.013 0.001 TYR I 33 ARG 0.005 0.000 ARG X 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 23) link_NAG-ASN : angle 3.72786 ( 69) link_ALPHA1-6 : bond 0.02015 ( 2) link_ALPHA1-6 : angle 2.90244 ( 6) link_BETA1-4 : bond 0.00776 ( 26) link_BETA1-4 : angle 2.62070 ( 78) link_ALPHA1-3 : bond 0.01214 ( 5) link_ALPHA1-3 : angle 2.72268 ( 15) hydrogen bonds : bond 0.03660 ( 682) hydrogen bonds : angle 5.03761 ( 1866) SS BOND : bond 0.00373 ( 31) SS BOND : angle 1.16764 ( 62) covalent geometry : bond 0.00261 (19071) covalent geometry : angle 0.65119 (25946) *********************** 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 226 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8189 (mmm) cc_final: 0.7617 (mmt) REVERT: J 52 VAL cc_start: 0.8972 (m) cc_final: 0.8525 (p) REVERT: J 82 ASP cc_start: 0.6384 (m-30) cc_final: 0.6112 (m-30) REVERT: Y 534 SER cc_start: 0.8900 (p) cc_final: 0.8697 (t) outliers start: 11 outliers final: 7 residues processed: 222 average time/residue: 0.2748 time to fit residues: 97.8334 Evaluate side-chains 187 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 418 CYS 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 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 22 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 203 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.105569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081952 restraints weight = 45895.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.083316 restraints weight = 39242.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.083948 restraints weight = 32038.601| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19158 Z= 0.131 Angle : 0.655 14.981 26176 Z= 0.308 Chirality : 0.047 0.448 3136 Planarity : 0.003 0.048 3203 Dihedral : 12.090 114.622 3662 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.67 % Favored : 94.24 % Rotamer: Outliers : 1.61 % Allowed : 12.82 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2274 helix: 1.58 (0.25), residues: 446 sheet: -0.51 (0.21), residues: 658 loop : -1.33 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Z 631 HIS 0.005 0.001 HIS A 72 PHE 0.025 0.001 PHE B 376 TYR 0.017 0.001 TYR B 40 ARG 0.004 0.000 ARG J 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 23) link_NAG-ASN : angle 3.46434 ( 69) link_ALPHA1-6 : bond 0.02006 ( 2) link_ALPHA1-6 : angle 2.87183 ( 6) link_BETA1-4 : bond 0.00659 ( 26) link_BETA1-4 : angle 2.44020 ( 78) link_ALPHA1-3 : bond 0.01273 ( 5) link_ALPHA1-3 : angle 2.14681 ( 15) hydrogen bonds : bond 0.03387 ( 682) hydrogen bonds : angle 4.87758 ( 1866) SS BOND : bond 0.00440 ( 31) SS BOND : angle 1.12722 ( 62) covalent geometry : bond 0.00293 (19071) covalent geometry : angle 0.61307 (25946) *********************** 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 233 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ASP cc_start: 0.7614 (p0) cc_final: 0.7384 (p0) REVERT: C 435 TYR cc_start: 0.7378 (t80) cc_final: 0.7095 (t80) REVERT: I 96 ASP cc_start: 0.7877 (p0) cc_final: 0.7603 (p0) REVERT: I 98 ASP cc_start: 0.8465 (p0) cc_final: 0.7977 (p0) REVERT: L 36 TYR cc_start: 0.8778 (m-80) cc_final: 0.8547 (m-80) REVERT: P 52 ASP cc_start: 0.6615 (t0) cc_final: 0.6332 (m-30) outliers start: 31 outliers final: 15 residues processed: 222 average time/residue: 0.3497 time to fit residues: 130.4514 Evaluate side-chains 185 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL 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 418 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 37 ILE 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 Q residue 52 VAL 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 34 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 180 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN C 478 ASN J 6 GLN Y 650 GLN Z 637 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.101352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078994 restraints weight = 47365.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.078319 restraints weight = 47295.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078845 restraints weight = 47547.039| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 19158 Z= 0.287 Angle : 0.750 15.629 26176 Z= 0.360 Chirality : 0.049 0.435 3136 Planarity : 0.004 0.052 3203 Dihedral : 10.883 111.739 3662 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.17 % Favored : 92.70 % Rotamer: Outliers : 2.28 % Allowed : 15.89 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.18), residues: 2274 helix: 1.37 (0.25), residues: 443 sheet: -0.58 (0.21), residues: 648 loop : -1.41 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 479 HIS 0.005 0.001 HIS A 72 PHE 0.020 0.002 PHE B 376 TYR 0.021 0.002 TYR Z 638 ARG 0.008 0.001 ARG I 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 23) link_NAG-ASN : angle 3.75437 ( 69) link_ALPHA1-6 : bond 0.02037 ( 2) link_ALPHA1-6 : angle 2.75889 ( 6) link_BETA1-4 : bond 0.00600 ( 26) link_BETA1-4 : angle 2.35733 ( 78) link_ALPHA1-3 : bond 0.01152 ( 5) link_ALPHA1-3 : angle 2.51925 ( 15) hydrogen bonds : bond 0.03922 ( 682) hydrogen bonds : angle 5.12916 ( 1866) SS BOND : bond 0.00479 ( 31) SS BOND : angle 1.21196 ( 62) covalent geometry : bond 0.00660 (19071) covalent geometry : angle 0.70981 (25946) *********************** 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 218 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8450 (t0) cc_final: 0.8055 (t0) outliers start: 44 outliers final: 20 residues processed: 207 average time/residue: 0.2730 time to fit residues: 92.4036 Evaluate side-chains 178 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 2.288 ------------------------------------------------------------------------------- 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 B residue 446 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 331 CYS Chi-restraints excluded: chain C residue 373 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 52 VAL 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 632 ASP Chi-restraints excluded: chain Y residue 595 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 85 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 136 optimal weight: 0.0970 chunk 123 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN L 79 GLN ** Z 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.104177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.081203 restraints weight = 46718.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.081837 restraints weight = 41425.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.082531 restraints weight = 35200.160| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19158 Z= 0.130 Angle : 0.661 15.171 26176 Z= 0.314 Chirality : 0.047 0.489 3136 Planarity : 0.003 0.050 3203 Dihedral : 10.187 111.472 3662 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 1.66 % Allowed : 18.17 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2274 helix: 1.67 (0.25), residues: 442 sheet: -0.56 (0.20), residues: 677 loop : -1.32 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 479 HIS 0.006 0.001 HIS A 72 PHE 0.019 0.001 PHE B 376 TYR 0.014 0.001 TYR Z 638 ARG 0.004 0.000 ARG X 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 23) link_NAG-ASN : angle 3.50962 ( 69) link_ALPHA1-6 : bond 0.02070 ( 2) link_ALPHA1-6 : angle 2.87932 ( 6) link_BETA1-4 : bond 0.00611 ( 26) link_BETA1-4 : angle 2.18267 ( 78) link_ALPHA1-3 : bond 0.01299 ( 5) link_ALPHA1-3 : angle 2.32596 ( 15) hydrogen bonds : bond 0.03383 ( 682) hydrogen bonds : angle 4.91334 ( 1866) SS BOND : bond 0.00412 ( 31) SS BOND : angle 1.13013 ( 62) covalent geometry : bond 0.00291 (19071) covalent geometry : angle 0.62085 (25946) *********************** 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 213 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8345 (t0) cc_final: 0.8006 (t0) REVERT: A 475 MET cc_start: 0.8287 (mmm) cc_final: 0.7743 (mmt) REVERT: H 33 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: I 98 ASP cc_start: 0.8443 (p0) cc_final: 0.7951 (p0) REVERT: Q 92 THR cc_start: 0.8749 (p) cc_final: 0.8145 (t) REVERT: X 530 MET cc_start: 0.8098 (mmt) cc_final: 0.7840 (mmt) REVERT: Y 635 ILE cc_start: 0.9336 (mm) cc_final: 0.9131 (tt) outliers start: 32 outliers final: 18 residues processed: 205 average time/residue: 0.2806 time to fit residues: 93.7665 Evaluate side-chains 177 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 44 VAL Chi-restraints excluded: chain C residue 294 ILE 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 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 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 Y residue 595 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 170 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 183 optimal weight: 0.0040 chunk 58 optimal weight: 0.8980 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.102866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079877 restraints weight = 46951.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.080363 restraints weight = 42052.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.080781 restraints weight = 37268.980| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1794 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= 0.182 Angle : 0.686 15.249 26176 Z= 0.326 Chirality : 0.047 0.470 3136 Planarity : 0.003 0.051 3203 Dihedral : 9.855 109.935 3662 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.90 % Favored : 93.01 % Rotamer: Outliers : 2.60 % Allowed : 18.90 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.18), residues: 2274 helix: 1.58 (0.25), residues: 448 sheet: -0.57 (0.21), residues: 667 loop : -1.34 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 479 HIS 0.004 0.001 HIS A 72 PHE 0.017 0.001 PHE B 376 TYR 0.018 0.002 TYR Z 638 ARG 0.005 0.000 ARG X 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 23) link_NAG-ASN : angle 3.52695 ( 69) link_ALPHA1-6 : bond 0.02048 ( 2) link_ALPHA1-6 : angle 2.80651 ( 6) link_BETA1-4 : bond 0.00595 ( 26) link_BETA1-4 : angle 2.15143 ( 78) link_ALPHA1-3 : bond 0.01204 ( 5) link_ALPHA1-3 : angle 2.45208 ( 15) hydrogen bonds : bond 0.03491 ( 682) hydrogen bonds : angle 4.92497 ( 1866) SS BOND : bond 0.00812 ( 31) SS BOND : angle 1.68738 ( 62) covalent geometry : bond 0.00420 (19071) covalent geometry : angle 0.64420 (25946) *********************** 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 217 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8426 (t0) cc_final: 0.8075 (t0) REVERT: H 33 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: I 98 ASP cc_start: 0.8448 (p0) cc_final: 0.7990 (p0) REVERT: Q 36 TYR cc_start: 0.9077 (m-80) cc_final: 0.8866 (m-80) REVERT: Q 92 THR cc_start: 0.8730 (p) cc_final: 0.8170 (t) REVERT: X 530 MET cc_start: 0.8161 (mmt) cc_final: 0.7884 (mmt) outliers start: 50 outliers final: 33 residues processed: 203 average time/residue: 0.2544 time to fit residues: 84.8771 Evaluate side-chains 193 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.903 ------------------------------------------------------------------------------- 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 218 CYS 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 107 ASP Chi-restraints excluded: chain C residue 123 THR 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 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 3 VAL 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 Y residue 595 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 30 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 228 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 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 = 0.3568 r_free = 0.3568 target = 0.101882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079445 restraints weight = 46993.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079710 restraints weight = 43400.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.080332 restraints weight = 40406.597| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19158 Z= 0.224 Angle : 0.716 15.350 26176 Z= 0.344 Chirality : 0.048 0.477 3136 Planarity : 0.004 0.051 3203 Dihedral : 9.695 109.137 3662 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.43 % Favored : 92.48 % Rotamer: Outliers : 2.44 % Allowed : 19.78 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2274 helix: 1.64 (0.25), residues: 437 sheet: -0.55 (0.21), residues: 659 loop : -1.37 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 45 HIS 0.005 0.001 HIS A 72 PHE 0.019 0.002 PHE B 376 TYR 0.017 0.002 TYR Z 638 ARG 0.006 0.000 ARG I 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 23) link_NAG-ASN : angle 3.61126 ( 69) link_ALPHA1-6 : bond 0.02167 ( 2) link_ALPHA1-6 : angle 2.83686 ( 6) link_BETA1-4 : bond 0.00601 ( 26) link_BETA1-4 : angle 2.14784 ( 78) link_ALPHA1-3 : bond 0.01113 ( 5) link_ALPHA1-3 : angle 2.48344 ( 15) hydrogen bonds : bond 0.03680 ( 682) hydrogen bonds : angle 4.99578 ( 1866) SS BOND : bond 0.00537 ( 31) SS BOND : angle 1.58596 ( 62) covalent geometry : bond 0.00520 (19071) covalent geometry : angle 0.67627 (25946) *********************** 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 208 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8442 (t0) cc_final: 0.8143 (t0) REVERT: H 33 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7129 (m-10) REVERT: I 98 ASP cc_start: 0.8466 (p0) cc_final: 0.8027 (p0) REVERT: Q 36 TYR cc_start: 0.9108 (m-80) cc_final: 0.8862 (m-80) REVERT: Q 92 THR cc_start: 0.8730 (p) cc_final: 0.8177 (t) REVERT: X 530 MET cc_start: 0.8158 (mmt) cc_final: 0.7895 (mmt) outliers start: 47 outliers final: 37 residues processed: 195 average time/residue: 0.2528 time to fit residues: 81.3837 Evaluate side-chains 195 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 2.065 ------------------------------------------------------------------------------- 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 A residue 491 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 CYS 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 107 ASP Chi-restraints excluded: chain C residue 123 THR 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 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 I residue 87 THR Chi-restraints excluded: chain J residue 3 VAL 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 Y residue 595 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 133 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 42 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 = 0.3604 r_free = 0.3604 target = 0.104070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.080803 restraints weight = 46836.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.081796 restraints weight = 39923.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.082194 restraints weight = 35378.682| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19158 Z= 0.133 Angle : 0.670 15.168 26176 Z= 0.320 Chirality : 0.047 0.502 3136 Planarity : 0.003 0.050 3203 Dihedral : 9.309 107.701 3662 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 2.28 % Allowed : 20.20 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2274 helix: 1.66 (0.25), residues: 452 sheet: -0.46 (0.21), residues: 656 loop : -1.35 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 69 HIS 0.006 0.001 HIS B 374 PHE 0.018 0.001 PHE B 376 TYR 0.012 0.001 TYR Z 638 ARG 0.010 0.000 ARG J 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 23) link_NAG-ASN : angle 3.47838 ( 69) link_ALPHA1-6 : bond 0.02219 ( 2) link_ALPHA1-6 : angle 2.87052 ( 6) link_BETA1-4 : bond 0.00612 ( 26) link_BETA1-4 : angle 2.05877 ( 78) link_ALPHA1-3 : bond 0.01200 ( 5) link_ALPHA1-3 : angle 2.33056 ( 15) hydrogen bonds : bond 0.03311 ( 682) hydrogen bonds : angle 4.82393 ( 1866) SS BOND : bond 0.00521 ( 31) SS BOND : angle 1.39369 ( 62) covalent geometry : bond 0.00304 (19071) covalent geometry : angle 0.63162 (25946) *********************** 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 216 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8393 (t0) cc_final: 0.8136 (t0) REVERT: H 33 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7129 (m-10) REVERT: J 36 TYR cc_start: 0.8887 (m-80) cc_final: 0.8381 (m-10) REVERT: Q 92 THR cc_start: 0.8667 (p) cc_final: 0.8056 (t) REVERT: X 621 GLU cc_start: 0.8199 (tp30) cc_final: 0.7975 (tp30) outliers start: 44 outliers final: 29 residues processed: 204 average time/residue: 0.2593 time to fit residues: 87.5426 Evaluate side-chains 193 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 218 CYS 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 44 VAL 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 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 87 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 59 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.102178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.079115 restraints weight = 47182.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.079162 restraints weight = 41587.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079902 restraints weight = 38294.557| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19158 Z= 0.205 Angle : 0.711 15.224 26176 Z= 0.340 Chirality : 0.047 0.477 3136 Planarity : 0.004 0.051 3203 Dihedral : 9.233 105.291 3662 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.61 % Rotamer: Outliers : 2.13 % Allowed : 20.77 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.18), residues: 2274 helix: 1.53 (0.25), residues: 452 sheet: -0.55 (0.21), residues: 660 loop : -1.35 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 479 HIS 0.005 0.001 HIS A 72 PHE 0.017 0.002 PHE B 376 TYR 0.017 0.002 TYR B 40 ARG 0.005 0.000 ARG X 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 23) link_NAG-ASN : angle 3.56233 ( 69) link_ALPHA1-6 : bond 0.02118 ( 2) link_ALPHA1-6 : angle 2.78351 ( 6) link_BETA1-4 : bond 0.00618 ( 26) link_BETA1-4 : angle 2.11099 ( 78) link_ALPHA1-3 : bond 0.01095 ( 5) link_ALPHA1-3 : angle 2.48528 ( 15) hydrogen bonds : bond 0.03571 ( 682) hydrogen bonds : angle 4.92201 ( 1866) SS BOND : bond 0.00510 ( 31) SS BOND : angle 1.47252 ( 62) covalent geometry : bond 0.00477 (19071) covalent geometry : angle 0.67254 (25946) *********************** 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 207 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8470 (t0) cc_final: 0.8173 (t0) REVERT: H 33 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.6944 (m-10) REVERT: Q 92 THR cc_start: 0.8748 (p) cc_final: 0.8244 (t) REVERT: X 530 MET cc_start: 0.8161 (mmt) cc_final: 0.7838 (mmt) outliers start: 41 outliers final: 37 residues processed: 199 average time/residue: 0.2647 time to fit residues: 86.3650 Evaluate side-chains 198 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 2.113 ------------------------------------------------------------------------------- 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 A residue 491 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 CYS 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 107 ASP 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 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 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 87 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 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 641 ILE Chi-restraints excluded: chain Y residue 595 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 67 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 425 ASN X 591 GLN ** Z 616 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 = 0.3528 r_free = 0.3528 target = 0.099514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077386 restraints weight = 47885.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.076501 restraints weight = 47785.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077283 restraints weight = 49474.619| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 19158 Z= 0.360 Angle : 0.848 15.838 26176 Z= 0.414 Chirality : 0.051 0.479 3136 Planarity : 0.005 0.056 3203 Dihedral : 9.600 108.544 3662 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.49 % Favored : 91.38 % Rotamer: Outliers : 2.23 % Allowed : 20.98 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.18), residues: 2274 helix: 1.02 (0.25), residues: 443 sheet: -0.70 (0.21), residues: 636 loop : -1.62 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 479 HIS 0.005 0.001 HIS J 52D PHE 0.023 0.003 PHE J 87 TYR 0.024 0.003 TYR Z 638 ARG 0.010 0.001 ARG H 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 23) link_NAG-ASN : angle 4.00448 ( 69) link_ALPHA1-6 : bond 0.02047 ( 2) link_ALPHA1-6 : angle 2.72833 ( 6) link_BETA1-4 : bond 0.00670 ( 26) link_BETA1-4 : angle 2.31377 ( 78) link_ALPHA1-3 : bond 0.00878 ( 5) link_ALPHA1-3 : angle 2.66624 ( 15) hydrogen bonds : bond 0.04382 ( 682) hydrogen bonds : angle 5.40712 ( 1866) SS BOND : bond 0.00556 ( 31) SS BOND : angle 1.62149 ( 62) covalent geometry : bond 0.00832 (19071) covalent geometry : angle 0.80875 (25946) ********************** 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 205 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 2.230 Fit side-chains revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8553 (t0) cc_final: 0.8248 (t0) REVERT: H 33 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.6948 (m-10) REVERT: I 98 ASP cc_start: 0.8455 (p0) cc_final: 0.8031 (p0) REVERT: X 530 MET cc_start: 0.8143 (mmt) cc_final: 0.7808 (mmt) outliers start: 43 outliers final: 36 residues processed: 196 average time/residue: 0.2560 time to fit residues: 83.8568 Evaluate side-chains 193 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 2.104 ------------------------------------------------------------------------------- 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 A residue 491 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 CYS 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 44 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 257 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 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 87 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 96 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 154 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 196 optimal weight: 8.9990 chunk 15 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.103292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.080464 restraints weight = 46785.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.080435 restraints weight = 41162.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.081143 restraints weight = 37850.687| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19158 Z= 0.135 Angle : 0.711 15.489 26176 Z= 0.341 Chirality : 0.047 0.522 3136 Planarity : 0.003 0.051 3203 Dihedral : 8.987 103.991 3662 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.02 % Favored : 93.89 % Rotamer: Outliers : 1.77 % Allowed : 21.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2274 helix: 1.48 (0.25), residues: 452 sheet: -0.55 (0.21), residues: 660 loop : -1.43 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 69 HIS 0.005 0.001 HIS A 72 PHE 0.017 0.001 PHE B 376 TYR 0.022 0.001 TYR C 173 ARG 0.008 0.001 ARG X 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 23) link_NAG-ASN : angle 3.63174 ( 69) link_ALPHA1-6 : bond 0.02267 ( 2) link_ALPHA1-6 : angle 2.92752 ( 6) link_BETA1-4 : bond 0.00611 ( 26) link_BETA1-4 : angle 2.03531 ( 78) link_ALPHA1-3 : bond 0.01189 ( 5) link_ALPHA1-3 : angle 2.36420 ( 15) hydrogen bonds : bond 0.03481 ( 682) hydrogen bonds : angle 4.94696 ( 1866) SS BOND : bond 0.00547 ( 31) SS BOND : angle 1.31316 ( 62) covalent geometry : bond 0.00303 (19071) covalent geometry : angle 0.67344 (25946) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5268.46 seconds wall clock time: 93 minutes 45.00 seconds (5625.00 seconds total)