Starting phenix.real_space_refine on Wed Mar 4 23:15:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uds_26458/03_2026/7uds_26458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uds_26458/03_2026/7uds_26458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uds_26458/03_2026/7uds_26458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uds_26458/03_2026/7uds_26458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uds_26458/03_2026/7uds_26458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uds_26458/03_2026/7uds_26458.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 10672 2.51 5 N 2837 2.21 5 O 3418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17032 Number of models: 1 Model: "" Number of chains: 32 Chain: "D" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1616 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "F" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1616 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "L" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "H" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1616 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "G" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "E" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "A" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1093 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 3 Chain: "C" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1093 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 3 Chain: "B" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1093 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 3 Chain: "a" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1133 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "c" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1133 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "b" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1133 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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: 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: "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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "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: 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: "T" 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.88, per 1000 atoms: 0.23 Number of scatterers: 17032 At special positions: 0 Unit cell: (209.336, 198.376, 89.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3418 8.00 N 2837 7.00 C 10672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 131 " - pdb=" SG CYS L 191 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 191 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 191 " distance=2.04 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.04 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.03 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.05 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.03 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.04 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " 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 I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A 301 " - " ASN A 166 " " NAG A 302 " - " ASN A 118 " " NAG B 301 " - " ASN B 108 " " NAG B 302 " - " ASN B 166 " " NAG B 303 " - " ASN B 118 " " NAG C 301 " - " ASN C 166 " " NAG C 302 " - " ASN C 118 " " NAG I 1 " - " ASN A 78 " " NAG J 1 " - " ASN A 88 " " NAG K 1 " - " ASN A 98 " " NAG M 1 " - " ASN A 108 " " NAG N 1 " - " ASN A 223 " " NAG O 1 " - " ASN C 78 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 98 " " NAG R 1 " - " ASN C 108 " " NAG S 1 " - " ASN C 223 " " NAG T 1 " - " ASN B 78 " " NAG U 1 " - " ASN B 88 " " NAG V 1 " - " ASN B 98 " " NAG W 1 " - " ASN B 223 " " NAG a 501 " - " ASN a 372 " " NAG b 501 " - " ASN b 372 " " NAG c 501 " - " ASN c 372 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 569.5 milliseconds 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3942 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 40 sheets defined 23.2% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.565A pdb=" N LYS D 31 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 62 through 65 removed outlier: 4.145A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.516A pdb=" N LYS F 31 " --> pdb=" O ASN F 28 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.531A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.997A pdb=" N PHE L 82 " --> pdb=" O PRO L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 125 Processing helix chain 'L' and resid 179 through 185 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.510A pdb=" N LYS H 31 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 194 through 200 Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.953A pdb=" N PHE G 82 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 125 Processing helix chain 'G' and resid 179 through 185 Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.955A pdb=" N PHE E 82 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 125 Processing helix chain 'E' and resid 179 through 185 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.766A pdb=" N THR A 76 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 4.019A pdb=" N ASN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.553A pdb=" N MET A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.078A pdb=" N LYS A 160 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 237 through 244 Processing helix chain 'C' and resid 73 through 78 removed outlier: 4.026A pdb=" N THR C 76 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 4.057A pdb=" N ASN C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 removed outlier: 3.559A pdb=" N MET C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 4.044A pdb=" N LYS C 160 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 237 through 244 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.850A pdb=" N THR B 76 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 4.028A pdb=" N ASN B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.683A pdb=" N MET B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 removed outlier: 4.078A pdb=" N LYS B 160 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 299 through 302 Processing helix chain 'a' and resid 308 through 324 Processing helix chain 'a' and resid 332 through 344 removed outlier: 3.529A pdb=" N ILE a 336 " --> pdb=" O SER a 332 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN a 341 " --> pdb=" O ASN a 337 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA a 342 " --> pdb=" O LYS a 338 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE a 344 " --> pdb=" O VAL a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 358 Processing helix chain 'a' and resid 395 through 397 No H-bonds generated for 'chain 'a' and resid 395 through 397' Processing helix chain 'a' and resid 398 through 414 removed outlier: 3.620A pdb=" N ILE a 402 " --> pdb=" O PHE a 398 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU a 414 " --> pdb=" O ILE a 410 " (cutoff:3.500A) Processing helix chain 'c' and resid 293 through 298 Processing helix chain 'c' and resid 299 through 302 removed outlier: 3.588A pdb=" N GLU c 302 " --> pdb=" O LYS c 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 299 through 302' Processing helix chain 'c' and resid 308 through 325 Processing helix chain 'c' and resid 333 through 344 removed outlier: 4.047A pdb=" N ASN c 341 " --> pdb=" O ASN c 337 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA c 342 " --> pdb=" O LYS c 338 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE c 344 " --> pdb=" O VAL c 340 " (cutoff:3.500A) Processing helix chain 'c' and resid 345 through 357 Processing helix chain 'c' and resid 394 through 397 Processing helix chain 'c' and resid 398 through 414 removed outlier: 3.520A pdb=" N ILE c 402 " --> pdb=" O PHE c 398 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU c 414 " --> pdb=" O ILE c 410 " (cutoff:3.500A) Processing helix chain 'b' and resid 293 through 298 Processing helix chain 'b' and resid 299 through 302 removed outlier: 3.650A pdb=" N GLU b 302 " --> pdb=" O LYS b 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 299 through 302' Processing helix chain 'b' and resid 308 through 324 Processing helix chain 'b' and resid 332 through 344 removed outlier: 3.573A pdb=" N ILE b 336 " --> pdb=" O SER b 332 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN b 341 " --> pdb=" O ASN b 337 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA b 342 " --> pdb=" O LYS b 338 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE b 344 " --> pdb=" O VAL b 340 " (cutoff:3.500A) Processing helix chain 'b' and resid 345 through 358 Processing helix chain 'b' and resid 398 through 414 removed outlier: 3.595A pdb=" N ILE b 402 " --> pdb=" O PHE b 398 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU b 414 " --> pdb=" O ILE b 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.786A pdb=" N ASN D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.952A pdb=" N ARG D 98 " --> pdb=" O ASP D 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 128 through 132 Processing sheet with id=AA5, first strand: chain 'D' and resid 128 through 132 Processing sheet with id=AA6, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.871A pdb=" N MET F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'F' and resid 128 through 132 removed outlier: 5.878A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AB3, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.644A pdb=" N ASP L 102 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU L 32 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR L 48 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 111 through 115 Processing sheet with id=AB6, first strand: chain 'L' and resid 141 through 147 Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.896A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.970A pdb=" N LEU H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE H 100 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ALA H 108 " --> pdb=" O ILE H 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'G' and resid 9 through 11 removed outlier: 3.753A pdb=" N ASP G 102 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU G 32 " --> pdb=" O TYR G 48 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR G 48 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP G 34 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 111 through 115 Processing sheet with id=AC7, first strand: chain 'G' and resid 141 through 147 Processing sheet with id=AC8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.548A pdb=" N ASP E 102 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP E 34 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 111 through 115 Processing sheet with id=AD2, first strand: chain 'E' and resid 141 through 147 Processing sheet with id=AD3, first strand: chain 'A' and resid 67 through 71 Processing sheet with id=AD4, first strand: chain 'A' and resid 83 through 88 removed outlier: 3.548A pdb=" N LYS A 87 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 67 through 71 Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 88 removed outlier: 3.686A pdb=" N LYS C 87 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N HIS C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 67 through 71 Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 88 removed outlier: 3.613A pdb=" N TYR B 93 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 87 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'a' and resid 387 through 388 Processing sheet with id=AE1, first strand: chain 'c' and resid 278 through 279 removed outlier: 3.704A pdb=" N LEU c 279 " --> pdb=" O LYS c 290 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS c 290 " --> pdb=" O LEU c 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'c' and resid 387 through 388 Processing sheet with id=AE3, first strand: chain 'b' and resid 278 through 279 removed outlier: 3.748A pdb=" N LEU b 279 " --> pdb=" O LYS b 290 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS b 290 " --> pdb=" O LEU b 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'b' and resid 387 through 388 741 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5361 1.35 - 1.47: 4536 1.47 - 1.60: 7317 1.60 - 1.73: 1 1.73 - 1.85: 153 Bond restraints: 17368 Sorted by residual: bond pdb=" C1 MAN V 4 " pdb=" C2 MAN V 4 " ideal model delta sigma weight residual 1.526 1.620 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 NAG A 301 " pdb=" O5 NAG A 301 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG C 301 " pdb=" O5 NAG C 301 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 MAN V 4 " pdb=" O5 MAN V 4 " ideal model delta sigma weight residual 1.399 1.474 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 17363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 23059 2.35 - 4.70: 416 4.70 - 7.05: 50 7.05 - 9.39: 7 9.39 - 11.74: 2 Bond angle restraints: 23534 Sorted by residual: angle pdb=" C SER G 29 " pdb=" CA SER G 29 " pdb=" CB SER G 29 " ideal model delta sigma weight residual 117.23 110.83 6.40 1.36e+00 5.41e-01 2.21e+01 angle pdb=" CA CYS c 291 " pdb=" CB CYS c 291 " pdb=" SG CYS c 291 " ideal model delta sigma weight residual 114.40 122.17 -7.77 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA SER G 29 " pdb=" C SER G 29 " pdb=" N SER G 30 " ideal model delta sigma weight residual 119.98 117.11 2.87 8.50e-01 1.38e+00 1.14e+01 angle pdb=" N TRP a 385 " pdb=" CA TRP a 385 " pdb=" C TRP a 385 " ideal model delta sigma weight residual 110.55 106.31 4.24 1.35e+00 5.49e-01 9.85e+00 angle pdb=" CA CYS a 291 " pdb=" CB CYS a 291 " pdb=" SG CYS a 291 " ideal model delta sigma weight residual 114.40 121.28 -6.88 2.30e+00 1.89e-01 8.94e+00 ... (remaining 23529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.17: 10280 23.17 - 46.33: 692 46.33 - 69.50: 89 69.50 - 92.67: 48 92.67 - 115.84: 42 Dihedral angle restraints: 11151 sinusoidal: 5052 harmonic: 6099 Sorted by residual: dihedral pdb=" CB CYS c 363 " pdb=" SG CYS c 363 " pdb=" SG CYS c 384 " pdb=" CB CYS c 384 " ideal model delta sinusoidal sigma weight residual -86.00 -170.32 84.32 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS b 363 " pdb=" SG CYS b 363 " pdb=" SG CYS b 384 " pdb=" CB CYS b 384 " ideal model delta sinusoidal sigma weight residual -86.00 -168.32 82.32 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS a 363 " pdb=" SG CYS a 363 " pdb=" SG CYS a 384 " pdb=" CB CYS a 384 " ideal model delta sinusoidal sigma weight residual -86.00 -168.12 82.12 1 1.00e+01 1.00e-02 8.28e+01 ... (remaining 11148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2273 0.057 - 0.113: 453 0.113 - 0.170: 66 0.170 - 0.227: 10 0.227 - 0.283: 10 Chirality restraints: 2812 Sorted by residual: chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B 78 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2809 not shown) Planarity restraints: 2936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 385 " -0.030 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP a 385 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP a 385 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP a 385 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP a 385 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP a 385 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 385 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 385 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP a 385 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 192 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO H 193 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO H 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 193 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 192 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO D 193 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 193 " -0.027 5.00e-02 4.00e+02 ... (remaining 2933 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 172 2.59 - 3.17: 13658 3.17 - 3.75: 24480 3.75 - 4.32: 34315 4.32 - 4.90: 56703 Nonbonded interactions: 129328 Sorted by model distance: nonbonded pdb=" OE1 GLU L 192 " pdb=" OG1 THR L 203 " model vdw 2.015 3.040 nonbonded pdb=" OE1 GLU G 192 " pdb=" OG1 THR G 203 " model vdw 2.097 3.040 nonbonded pdb=" O TRP F 106 " pdb=" OG SER G 90 " model vdw 2.127 3.040 nonbonded pdb=" OE1 GLU E 192 " pdb=" OG1 THR E 203 " model vdw 2.164 3.040 nonbonded pdb=" OG SER B 90 " pdb=" O7 NAG U 1 " model vdw 2.213 3.040 ... (remaining 129323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 66 through 302) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'K' selection = chain 'Q' selection = chain 'V' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.690 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 : 0.005 0.094 17448 Z= 0.226 Angle : 0.776 13.345 23747 Z= 0.363 Chirality : 0.049 0.283 2812 Planarity : 0.004 0.050 2912 Dihedral : 17.286 115.837 7128 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 2046 helix: 0.69 (0.29), residues: 345 sheet: 0.67 (0.19), residues: 783 loop : -1.22 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 95 TYR 0.019 0.002 TYR E 48 PHE 0.017 0.002 PHE G 70 TRP 0.073 0.002 TRP a 385 HIS 0.006 0.001 HIS a 353 Details of bonding type rmsd covalent geometry : bond 0.00486 (17368) covalent geometry : angle 0.74309 (23534) SS BOND : bond 0.00708 ( 27) SS BOND : angle 1.73256 ( 54) hydrogen bonds : bond 0.13650 ( 691) hydrogen bonds : angle 6.36723 ( 1941) link_ALPHA1-3 : bond 0.01221 ( 6) link_ALPHA1-3 : angle 2.22594 ( 18) link_ALPHA1-6 : bond 0.00739 ( 3) link_ALPHA1-6 : angle 1.60110 ( 9) link_BETA1-4 : bond 0.00775 ( 20) link_BETA1-4 : angle 2.28829 ( 60) link_NAG-ASN : bond 0.00443 ( 24) link_NAG-ASN : angle 3.19058 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 143 THR cc_start: 0.6360 (t) cc_final: 0.6067 (m) REVERT: H 153 TYR cc_start: 0.6062 (p90) cc_final: 0.5472 (p90) REVERT: G 3 MET cc_start: 0.7598 (mmm) cc_final: 0.7239 (mmm) REVERT: a 394 ASN cc_start: 0.7658 (p0) cc_final: 0.7441 (p0) REVERT: a 413 MET cc_start: 0.6709 (tmm) cc_final: 0.6452 (tmm) REVERT: c 286 GLU cc_start: 0.6091 (tm-30) cc_final: 0.5820 (tm-30) REVERT: b 350 MET cc_start: 0.7231 (mmm) cc_final: 0.6932 (mmm) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1192 time to fit residues: 50.1948 Evaluate side-chains 254 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS a 318 ASN ** a 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 318 ASN c 405 GLN b 318 ASN b 353 HIS b 364 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.173376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147973 restraints weight = 27766.549| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.51 r_work: 0.3779 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17448 Z= 0.197 Angle : 0.743 12.277 23747 Z= 0.355 Chirality : 0.047 0.269 2812 Planarity : 0.005 0.050 2912 Dihedral : 14.828 102.114 3321 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.92 % Allowed : 7.97 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 2046 helix: 0.51 (0.27), residues: 357 sheet: 0.59 (0.19), residues: 789 loop : -1.23 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 105 TYR 0.023 0.002 TYR F 94 PHE 0.018 0.002 PHE D 80 TRP 0.024 0.002 TRP a 385 HIS 0.005 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00455 (17368) covalent geometry : angle 0.70456 (23534) SS BOND : bond 0.00768 ( 27) SS BOND : angle 1.93954 ( 54) hydrogen bonds : bond 0.04293 ( 691) hydrogen bonds : angle 5.45446 ( 1941) link_ALPHA1-3 : bond 0.02215 ( 6) link_ALPHA1-3 : angle 3.37509 ( 18) link_ALPHA1-6 : bond 0.00921 ( 3) link_ALPHA1-6 : angle 2.14825 ( 9) link_BETA1-4 : bond 0.00699 ( 20) link_BETA1-4 : angle 2.10344 ( 60) link_NAG-ASN : bond 0.00460 ( 24) link_NAG-ASN : angle 3.12247 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 259 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 143 THR cc_start: 0.6424 (t) cc_final: 0.6145 (m) REVERT: H 153 TYR cc_start: 0.6249 (p90) cc_final: 0.5624 (p90) REVERT: G 81 ASP cc_start: 0.7054 (m-30) cc_final: 0.6810 (m-30) REVERT: B 81 MET cc_start: 0.6980 (mtp) cc_final: 0.6769 (mtp) REVERT: a 409 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5919 (mpp) REVERT: a 413 MET cc_start: 0.7018 (tmm) cc_final: 0.6566 (tmm) REVERT: c 286 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6383 (tm-30) REVERT: c 338 LYS cc_start: 0.8158 (ptmt) cc_final: 0.7876 (ptmt) REVERT: b 350 MET cc_start: 0.7648 (mmm) cc_final: 0.7404 (mpp) outliers start: 17 outliers final: 13 residues processed: 264 average time/residue: 0.1179 time to fit residues: 48.5007 Evaluate side-chains 264 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 250 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 42 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 141 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 353 HIS b 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.173823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.148778 restraints weight = 28097.612| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.40 r_work: 0.3793 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17448 Z= 0.166 Angle : 0.708 11.976 23747 Z= 0.334 Chirality : 0.045 0.263 2812 Planarity : 0.005 0.050 2912 Dihedral : 12.322 113.206 3321 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.41 % Allowed : 12.47 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.19), residues: 2046 helix: 0.50 (0.27), residues: 357 sheet: 0.57 (0.19), residues: 786 loop : -1.17 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 105 TYR 0.021 0.002 TYR F 94 PHE 0.019 0.002 PHE D 80 TRP 0.015 0.002 TRP a 385 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00380 (17368) covalent geometry : angle 0.66870 (23534) SS BOND : bond 0.00683 ( 27) SS BOND : angle 1.80611 ( 54) hydrogen bonds : bond 0.03901 ( 691) hydrogen bonds : angle 5.19469 ( 1941) link_ALPHA1-3 : bond 0.02501 ( 6) link_ALPHA1-3 : angle 3.25040 ( 18) link_ALPHA1-6 : bond 0.01295 ( 3) link_ALPHA1-6 : angle 2.18954 ( 9) link_BETA1-4 : bond 0.00714 ( 20) link_BETA1-4 : angle 1.95397 ( 60) link_NAG-ASN : bond 0.00360 ( 24) link_NAG-ASN : angle 3.21297 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 143 THR cc_start: 0.6358 (t) cc_final: 0.6063 (m) REVERT: H 153 TYR cc_start: 0.6349 (p90) cc_final: 0.5703 (p90) REVERT: G 81 ASP cc_start: 0.7277 (m-30) cc_final: 0.6986 (m-30) REVERT: a 286 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6938 (tm-30) REVERT: a 409 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6073 (mpp) REVERT: a 413 MET cc_start: 0.7229 (tmm) cc_final: 0.6809 (tmm) REVERT: c 286 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6713 (tm-30) REVERT: c 335 LEU cc_start: 0.7797 (tt) cc_final: 0.7595 (tp) REVERT: c 338 LYS cc_start: 0.8244 (ptmt) cc_final: 0.7980 (ptmt) REVERT: b 350 MET cc_start: 0.7854 (mmm) cc_final: 0.7370 (mmm) REVERT: b 409 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6187 (mpp) outliers start: 26 outliers final: 17 residues processed: 272 average time/residue: 0.1202 time to fit residues: 50.4282 Evaluate side-chains 271 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 0.0030 chunk 129 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 141 optimal weight: 0.0030 chunk 39 optimal weight: 3.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN a 405 GLN b 353 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.172962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.147946 restraints weight = 27868.531| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.42 r_work: 0.3800 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17448 Z= 0.159 Angle : 0.684 11.843 23747 Z= 0.324 Chirality : 0.045 0.267 2812 Planarity : 0.005 0.051 2912 Dihedral : 10.931 110.769 3321 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.84 % Allowed : 15.12 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 2046 helix: 0.58 (0.27), residues: 357 sheet: 0.55 (0.19), residues: 777 loop : -1.15 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.018 0.001 TYR G 48 PHE 0.012 0.001 PHE b 398 TRP 0.009 0.002 TRP a 385 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00363 (17368) covalent geometry : angle 0.64634 (23534) SS BOND : bond 0.00707 ( 27) SS BOND : angle 1.63065 ( 54) hydrogen bonds : bond 0.03739 ( 691) hydrogen bonds : angle 5.09680 ( 1941) link_ALPHA1-3 : bond 0.02396 ( 6) link_ALPHA1-3 : angle 3.42762 ( 18) link_ALPHA1-6 : bond 0.01492 ( 3) link_ALPHA1-6 : angle 2.20130 ( 9) link_BETA1-4 : bond 0.00679 ( 20) link_BETA1-4 : angle 1.95631 ( 60) link_NAG-ASN : bond 0.00347 ( 24) link_NAG-ASN : angle 2.97061 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 VAL cc_start: 0.7459 (OUTLIER) cc_final: 0.7256 (t) REVERT: D 64 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6777 (pp) REVERT: F 105 THR cc_start: 0.6613 (OUTLIER) cc_final: 0.6266 (m) REVERT: F 143 THR cc_start: 0.6388 (t) cc_final: 0.6128 (m) REVERT: H 153 TYR cc_start: 0.6419 (p90) cc_final: 0.4631 (p90) REVERT: G 81 ASP cc_start: 0.7200 (m-30) cc_final: 0.6923 (m-30) REVERT: A 138 THR cc_start: 0.7868 (t) cc_final: 0.7577 (p) REVERT: a 286 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6914 (tm-30) REVERT: a 409 MET cc_start: 0.6687 (mpp) cc_final: 0.6159 (mpp) REVERT: a 413 MET cc_start: 0.7261 (tmm) cc_final: 0.6853 (tmm) REVERT: c 286 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6829 (tm-30) REVERT: c 338 LYS cc_start: 0.8233 (ptmt) cc_final: 0.7968 (ptmt) REVERT: b 350 MET cc_start: 0.7764 (mmm) cc_final: 0.7236 (mmm) REVERT: b 409 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6245 (mpp) outliers start: 34 outliers final: 22 residues processed: 277 average time/residue: 0.1163 time to fit residues: 50.0553 Evaluate side-chains 275 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 10 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 116 optimal weight: 0.4980 chunk 196 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 HIS ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.171949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146886 restraints weight = 27801.737| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.43 r_work: 0.3790 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17448 Z= 0.191 Angle : 0.712 12.041 23747 Z= 0.337 Chirality : 0.046 0.271 2812 Planarity : 0.005 0.052 2912 Dihedral : 10.427 110.871 3321 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.33 % Allowed : 16.48 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 2046 helix: 0.54 (0.27), residues: 357 sheet: 0.59 (0.19), residues: 771 loop : -1.23 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.020 0.002 TYR G 48 PHE 0.013 0.002 PHE D 27 TRP 0.009 0.002 TRP b 282 HIS 0.006 0.001 HIS a 353 Details of bonding type rmsd covalent geometry : bond 0.00443 (17368) covalent geometry : angle 0.67416 (23534) SS BOND : bond 0.00787 ( 27) SS BOND : angle 1.78545 ( 54) hydrogen bonds : bond 0.03952 ( 691) hydrogen bonds : angle 5.14816 ( 1941) link_ALPHA1-3 : bond 0.02447 ( 6) link_ALPHA1-3 : angle 3.46601 ( 18) link_ALPHA1-6 : bond 0.01545 ( 3) link_ALPHA1-6 : angle 2.25543 ( 9) link_BETA1-4 : bond 0.00676 ( 20) link_BETA1-4 : angle 1.97393 ( 60) link_NAG-ASN : bond 0.00386 ( 24) link_NAG-ASN : angle 3.05990 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6788 (pp) REVERT: F 4 LEU cc_start: 0.7952 (mt) cc_final: 0.7639 (mp) REVERT: F 105 THR cc_start: 0.6601 (OUTLIER) cc_final: 0.6238 (m) REVERT: F 143 THR cc_start: 0.6416 (t) cc_final: 0.6152 (m) REVERT: H 110 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8310 (tp) REVERT: H 153 TYR cc_start: 0.6403 (p90) cc_final: 0.4621 (p90) REVERT: G 3 MET cc_start: 0.8001 (tpp) cc_final: 0.7426 (mmm) REVERT: G 81 ASP cc_start: 0.7262 (m-30) cc_final: 0.6975 (m-30) REVERT: A 138 THR cc_start: 0.7881 (t) cc_final: 0.7580 (p) REVERT: C 95 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7327 (mtt-85) REVERT: a 286 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6958 (tm-30) REVERT: a 307 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7261 (mm-30) REVERT: a 409 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6122 (mpp) REVERT: a 413 MET cc_start: 0.7369 (tmm) cc_final: 0.6951 (tmm) REVERT: c 286 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6841 (tm-30) REVERT: c 338 LYS cc_start: 0.8235 (ptmt) cc_final: 0.7956 (ptmt) REVERT: b 350 MET cc_start: 0.7765 (mmm) cc_final: 0.7326 (mmm) REVERT: b 409 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6207 (mpp) outliers start: 43 outliers final: 30 residues processed: 279 average time/residue: 0.1146 time to fit residues: 50.5686 Evaluate side-chains 285 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 335 LEU Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 140 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 188 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.171344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.146307 restraints weight = 27617.635| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.39 r_work: 0.3776 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17448 Z= 0.235 Angle : 0.765 12.431 23747 Z= 0.365 Chirality : 0.048 0.280 2812 Planarity : 0.005 0.053 2912 Dihedral : 10.348 110.235 3321 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.20 % Allowed : 17.34 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 2046 helix: 0.42 (0.27), residues: 357 sheet: 0.56 (0.19), residues: 795 loop : -1.42 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 105 TYR 0.023 0.002 TYR G 48 PHE 0.019 0.002 PHE H 68 TRP 0.011 0.002 TRP b 282 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00550 (17368) covalent geometry : angle 0.72221 (23534) SS BOND : bond 0.00900 ( 27) SS BOND : angle 2.59496 ( 54) hydrogen bonds : bond 0.04270 ( 691) hydrogen bonds : angle 5.27560 ( 1941) link_ALPHA1-3 : bond 0.02531 ( 6) link_ALPHA1-3 : angle 3.65928 ( 18) link_ALPHA1-6 : bond 0.01528 ( 3) link_ALPHA1-6 : angle 2.29539 ( 9) link_BETA1-4 : bond 0.00680 ( 20) link_BETA1-4 : angle 2.10319 ( 60) link_NAG-ASN : bond 0.00431 ( 24) link_NAG-ASN : angle 3.16791 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 268 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 VAL cc_start: 0.7423 (OUTLIER) cc_final: 0.7216 (t) REVERT: D 64 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6844 (pp) REVERT: D 132 LEU cc_start: 0.3661 (OUTLIER) cc_final: 0.2970 (tt) REVERT: F 105 THR cc_start: 0.6797 (OUTLIER) cc_final: 0.6429 (m) REVERT: H 87 ARG cc_start: 0.6532 (ttp-170) cc_final: 0.6316 (ttm170) REVERT: H 110 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8312 (tp) REVERT: H 153 TYR cc_start: 0.6431 (p90) cc_final: 0.4688 (p90) REVERT: G 81 ASP cc_start: 0.7340 (m-30) cc_final: 0.7101 (m-30) REVERT: A 138 THR cc_start: 0.7851 (t) cc_final: 0.7571 (p) REVERT: C 95 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7370 (mtt-85) REVERT: a 286 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6966 (tm-30) REVERT: a 307 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: a 409 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6149 (mpp) REVERT: a 413 MET cc_start: 0.7434 (tmm) cc_final: 0.7028 (tmm) REVERT: c 286 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6861 (tm-30) REVERT: c 338 LYS cc_start: 0.8255 (ptmt) cc_final: 0.7962 (ptmt) REVERT: b 350 MET cc_start: 0.7813 (mmm) cc_final: 0.7359 (mmm) REVERT: b 409 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6186 (mpp) outliers start: 59 outliers final: 43 residues processed: 301 average time/residue: 0.1123 time to fit residues: 52.8186 Evaluate side-chains 314 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 335 LEU Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 198 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 196 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 GLN b 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.171339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.146317 restraints weight = 27705.020| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.39 r_work: 0.3777 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17448 Z= 0.222 Angle : 0.755 12.437 23747 Z= 0.361 Chirality : 0.048 0.286 2812 Planarity : 0.005 0.053 2912 Dihedral : 10.167 109.945 3321 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.09 % Allowed : 18.37 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.19), residues: 2046 helix: 0.33 (0.27), residues: 357 sheet: 0.34 (0.19), residues: 819 loop : -1.41 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.022 0.002 TYR G 48 PHE 0.019 0.002 PHE H 68 TRP 0.011 0.002 TRP B 226 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00516 (17368) covalent geometry : angle 0.71203 (23534) SS BOND : bond 0.00867 ( 27) SS BOND : angle 2.47810 ( 54) hydrogen bonds : bond 0.04237 ( 691) hydrogen bonds : angle 5.27702 ( 1941) link_ALPHA1-3 : bond 0.02537 ( 6) link_ALPHA1-3 : angle 3.69758 ( 18) link_ALPHA1-6 : bond 0.01552 ( 3) link_ALPHA1-6 : angle 2.29573 ( 9) link_BETA1-4 : bond 0.00684 ( 20) link_BETA1-4 : angle 2.04553 ( 60) link_NAG-ASN : bond 0.00403 ( 24) link_NAG-ASN : angle 3.17668 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 269 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6839 (pp) REVERT: D 132 LEU cc_start: 0.3795 (OUTLIER) cc_final: 0.3112 (tt) REVERT: H 87 ARG cc_start: 0.6540 (ttp-170) cc_final: 0.6302 (ttm170) REVERT: H 110 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8304 (tp) REVERT: H 153 TYR cc_start: 0.6441 (p90) cc_final: 0.4691 (p90) REVERT: G 3 MET cc_start: 0.7859 (mmt) cc_final: 0.7457 (mmm) REVERT: G 133 LEU cc_start: 0.7448 (tt) cc_final: 0.7228 (tt) REVERT: A 138 THR cc_start: 0.7844 (t) cc_final: 0.7569 (p) REVERT: C 95 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7364 (mtt-85) REVERT: C 193 MET cc_start: 0.5601 (mmt) cc_final: 0.5366 (mmt) REVERT: B 189 THR cc_start: 0.7798 (p) cc_final: 0.7541 (p) REVERT: a 286 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6905 (tm-30) REVERT: a 307 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7188 (mm-30) REVERT: a 409 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.6144 (mpp) REVERT: c 286 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6895 (tm-30) REVERT: c 338 LYS cc_start: 0.8243 (ptmt) cc_final: 0.7949 (ptmt) REVERT: b 350 MET cc_start: 0.7786 (mmm) cc_final: 0.7371 (mmm) REVERT: b 409 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6177 (mpp) outliers start: 57 outliers final: 43 residues processed: 301 average time/residue: 0.1198 time to fit residues: 56.4355 Evaluate side-chains 317 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 267 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 278 CYS Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 335 LEU Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 56 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 113 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 341 ASN a 364 ASN b 353 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.171973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146970 restraints weight = 27893.713| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.42 r_work: 0.3782 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17448 Z= 0.183 Angle : 0.724 12.241 23747 Z= 0.344 Chirality : 0.046 0.278 2812 Planarity : 0.005 0.053 2912 Dihedral : 9.819 109.031 3321 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.31 % Allowed : 18.81 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.19), residues: 2046 helix: 0.42 (0.27), residues: 357 sheet: 0.45 (0.19), residues: 810 loop : -1.43 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.019 0.002 TYR G 48 PHE 0.016 0.002 PHE H 68 TRP 0.010 0.002 TRP B 226 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00418 (17368) covalent geometry : angle 0.68271 (23534) SS BOND : bond 0.00790 ( 27) SS BOND : angle 2.25082 ( 54) hydrogen bonds : bond 0.03963 ( 691) hydrogen bonds : angle 5.16992 ( 1941) link_ALPHA1-3 : bond 0.02591 ( 6) link_ALPHA1-3 : angle 3.67893 ( 18) link_ALPHA1-6 : bond 0.01581 ( 3) link_ALPHA1-6 : angle 2.27714 ( 9) link_BETA1-4 : bond 0.00672 ( 20) link_BETA1-4 : angle 1.95845 ( 60) link_NAG-ASN : bond 0.00344 ( 24) link_NAG-ASN : angle 3.05041 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 254 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6828 (pp) REVERT: D 132 LEU cc_start: 0.3781 (OUTLIER) cc_final: 0.3137 (tt) REVERT: F 105 THR cc_start: 0.6698 (OUTLIER) cc_final: 0.6336 (m) REVERT: H 110 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8302 (tp) REVERT: H 153 TYR cc_start: 0.6404 (p90) cc_final: 0.4612 (p90) REVERT: G 3 MET cc_start: 0.7916 (mmt) cc_final: 0.7577 (mmm) REVERT: G 133 LEU cc_start: 0.7405 (tt) cc_final: 0.7191 (tt) REVERT: C 95 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7336 (mtt-85) REVERT: a 286 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6895 (tm-30) REVERT: a 307 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7214 (mm-30) REVERT: a 409 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6167 (mpp) REVERT: c 286 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6912 (tm-30) REVERT: c 338 LYS cc_start: 0.8241 (ptmt) cc_final: 0.7962 (ptmt) REVERT: b 350 MET cc_start: 0.7773 (mmm) cc_final: 0.7367 (mmm) REVERT: b 409 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6119 (mpp) outliers start: 61 outliers final: 47 residues processed: 292 average time/residue: 0.1196 time to fit residues: 54.6171 Evaluate side-chains 305 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 278 CYS Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 335 LEU Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 109 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 160 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 197 optimal weight: 0.0770 chunk 80 optimal weight: 0.0570 chunk 193 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS b 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.172830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147712 restraints weight = 27867.507| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.42 r_work: 0.3798 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17448 Z= 0.145 Angle : 0.685 11.602 23747 Z= 0.325 Chirality : 0.045 0.261 2812 Planarity : 0.004 0.052 2912 Dihedral : 9.311 107.718 3321 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.93 % Allowed : 19.19 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 2046 helix: 0.53 (0.27), residues: 357 sheet: 0.51 (0.19), residues: 810 loop : -1.33 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.014 0.001 TYR G 48 PHE 0.012 0.001 PHE b 398 TRP 0.009 0.001 TRP B 226 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00323 (17368) covalent geometry : angle 0.64629 (23534) SS BOND : bond 0.00680 ( 27) SS BOND : angle 2.00209 ( 54) hydrogen bonds : bond 0.03605 ( 691) hydrogen bonds : angle 5.01202 ( 1941) link_ALPHA1-3 : bond 0.02636 ( 6) link_ALPHA1-3 : angle 3.65854 ( 18) link_ALPHA1-6 : bond 0.01648 ( 3) link_ALPHA1-6 : angle 2.22316 ( 9) link_BETA1-4 : bond 0.00666 ( 20) link_BETA1-4 : angle 1.83460 ( 60) link_NAG-ASN : bond 0.00321 ( 24) link_NAG-ASN : angle 2.89698 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6881 (pp) REVERT: D 132 LEU cc_start: 0.3734 (OUTLIER) cc_final: 0.3111 (tt) REVERT: F 105 THR cc_start: 0.6519 (OUTLIER) cc_final: 0.6308 (m) REVERT: H 110 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8324 (tp) REVERT: H 153 TYR cc_start: 0.6375 (p90) cc_final: 0.4568 (p90) REVERT: A 138 THR cc_start: 0.7873 (t) cc_final: 0.7613 (p) REVERT: C 95 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7285 (mtt-85) REVERT: a 286 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6865 (tm-30) REVERT: a 307 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: a 409 MET cc_start: 0.6659 (OUTLIER) cc_final: 0.6134 (mpp) REVERT: c 286 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6879 (tm-30) REVERT: c 338 LYS cc_start: 0.8228 (ptmt) cc_final: 0.7918 (ptmt) REVERT: b 350 MET cc_start: 0.7727 (mmm) cc_final: 0.7223 (mmm) REVERT: b 409 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6133 (mpp) outliers start: 54 outliers final: 37 residues processed: 285 average time/residue: 0.1174 time to fit residues: 52.1718 Evaluate side-chains 297 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 335 LEU Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 130 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 163 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** 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 = 0.4206 r_free = 0.4206 target = 0.171773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146930 restraints weight = 27541.617| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.39 r_work: 0.3781 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17448 Z= 0.204 Angle : 0.743 12.382 23747 Z= 0.352 Chirality : 0.047 0.266 2812 Planarity : 0.005 0.053 2912 Dihedral : 9.298 106.633 3321 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.76 % Allowed : 19.35 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 2046 helix: 0.45 (0.27), residues: 357 sheet: 0.57 (0.19), residues: 801 loop : -1.42 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.020 0.002 TYR G 48 PHE 0.014 0.002 PHE H 68 TRP 0.010 0.002 TRP b 385 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00472 (17368) covalent geometry : angle 0.70267 (23534) SS BOND : bond 0.00892 ( 27) SS BOND : angle 2.28567 ( 54) hydrogen bonds : bond 0.04012 ( 691) hydrogen bonds : angle 5.17573 ( 1941) link_ALPHA1-3 : bond 0.02650 ( 6) link_ALPHA1-3 : angle 3.71832 ( 18) link_ALPHA1-6 : bond 0.01640 ( 3) link_ALPHA1-6 : angle 2.21419 ( 9) link_BETA1-4 : bond 0.00663 ( 20) link_BETA1-4 : angle 2.03012 ( 60) link_NAG-ASN : bond 0.00356 ( 24) link_NAG-ASN : angle 3.05200 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6864 (pp) REVERT: D 132 LEU cc_start: 0.3779 (OUTLIER) cc_final: 0.3153 (tt) REVERT: F 105 THR cc_start: 0.6724 (OUTLIER) cc_final: 0.6511 (m) REVERT: H 87 ARG cc_start: 0.6553 (ttm170) cc_final: 0.6231 (ttm170) REVERT: H 110 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8303 (tp) REVERT: H 153 TYR cc_start: 0.6412 (p90) cc_final: 0.4647 (p90) REVERT: A 138 THR cc_start: 0.7876 (t) cc_final: 0.7595 (p) REVERT: C 95 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7360 (mtt-85) REVERT: a 286 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6849 (tm-30) REVERT: a 307 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7200 (mm-30) REVERT: a 409 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6157 (mpp) REVERT: c 286 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6908 (tm-30) REVERT: c 338 LYS cc_start: 0.8219 (ptmt) cc_final: 0.7926 (ptmt) REVERT: b 350 MET cc_start: 0.7746 (mmm) cc_final: 0.7299 (mmm) REVERT: b 353 HIS cc_start: 0.7815 (t70) cc_final: 0.7494 (t-90) REVERT: b 409 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6110 (mpp) outliers start: 51 outliers final: 38 residues processed: 283 average time/residue: 0.1244 time to fit residues: 54.5725 Evaluate side-chains 300 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 335 LEU Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 74 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 183 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 11 optimal weight: 0.0980 chunk 87 optimal weight: 0.5980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** 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 = 0.4227 r_free = 0.4227 target = 0.173387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148295 restraints weight = 27795.765| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.42 r_work: 0.3808 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17448 Z= 0.131 Angle : 0.676 12.710 23747 Z= 0.320 Chirality : 0.044 0.261 2812 Planarity : 0.004 0.052 2912 Dihedral : 8.851 105.615 3321 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.49 % Allowed : 19.84 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 2046 helix: 0.59 (0.27), residues: 357 sheet: 0.55 (0.19), residues: 810 loop : -1.25 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.013 0.001 TYR G 48 PHE 0.013 0.001 PHE b 398 TRP 0.008 0.001 TRP B 226 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00285 (17368) covalent geometry : angle 0.63939 (23534) SS BOND : bond 0.00628 ( 27) SS BOND : angle 1.90631 ( 54) hydrogen bonds : bond 0.03435 ( 691) hydrogen bonds : angle 4.95115 ( 1941) link_ALPHA1-3 : bond 0.02704 ( 6) link_ALPHA1-3 : angle 3.67494 ( 18) link_ALPHA1-6 : bond 0.01719 ( 3) link_ALPHA1-6 : angle 1.93100 ( 9) link_BETA1-4 : bond 0.00672 ( 20) link_BETA1-4 : angle 1.74376 ( 60) link_NAG-ASN : bond 0.00338 ( 24) link_NAG-ASN : angle 2.82734 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5150.85 seconds wall clock time: 88 minutes 42.58 seconds (5322.58 seconds total)