Starting phenix.real_space_refine on Tue Nov 18 12:08:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ds5_8909/11_2025/6ds5_8909_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ds5_8909/11_2025/6ds5_8909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ds5_8909/11_2025/6ds5_8909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ds5_8909/11_2025/6ds5_8909.map" model { file = "/net/cci-nas-00/data/ceres_data/6ds5_8909/11_2025/6ds5_8909_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ds5_8909/11_2025/6ds5_8909_neut.cif" } resolution = 3.8 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= 0.013 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 66 5.16 5 C 8866 2.51 5 N 2332 2.21 5 O 2706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13970 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" 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: "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: 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 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 Time building chain proxies: 3.18, per 1000 atoms: 0.23 Number of scatterers: 13970 At special positions: 0 Unit cell: (152.24, 153.12, 59.84, 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 66 16.00 O 2706 8.00 N 2332 7.00 C 8866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 82 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 82 " distance=2.04 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 82 " distance=2.03 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS D 82 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS F 74 " - pdb=" SG CYS F 82 " distance=2.03 Simple disulfide: pdb=" SG CYS G 74 " - pdb=" SG CYS G 82 " distance=2.03 Simple disulfide: pdb=" SG CYS H 74 " - pdb=" SG CYS H 82 " distance=2.03 Simple disulfide: pdb=" SG CYS I 74 " - pdb=" SG CYS I 82 " distance=2.03 Simple disulfide: pdb=" SG CYS J 74 " - pdb=" SG CYS J 82 " distance=2.03 Simple disulfide: pdb=" SG CYS K 74 " - pdb=" SG CYS K 82 " 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 BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG L 1 " - " ASN A 88 " " NAG M 1 " - " ASN B 88 " " NAG N 1 " - " ASN C 88 " " NAG O 1 " - " ASN D 88 " " NAG P 1 " - " ASN E 88 " " NAG Q 1 " - " ASN F 88 " " NAG R 1 " - " ASN G 88 " " NAG S 1 " - " ASN H 88 " " NAG T 1 " - " ASN I 88 " " NAG U 1 " - " ASN J 88 " " NAG V 1 " - " ASN K 88 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 639.9 milliseconds 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 22 sheets defined 18.8% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 117 through 123 removed outlier: 4.129A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR A 192 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 193 " --> pdb=" O ASN A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 193' Processing helix chain 'B' and resid 117 through 123 removed outlier: 4.184A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR B 192 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 193 " --> pdb=" O ASN B 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 193' Processing helix chain 'C' and resid 117 through 123 removed outlier: 4.204A pdb=" N LEU C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR C 192 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL C 193 " --> pdb=" O ASN C 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 193' Processing helix chain 'D' and resid 117 through 123 removed outlier: 4.156A pdb=" N LEU D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR D 192 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL D 193 " --> pdb=" O ASN D 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 189 through 193' Processing helix chain 'E' and resid 117 through 123 removed outlier: 4.179A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR E 192 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL E 193 " --> pdb=" O ASN E 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 189 through 193' Processing helix chain 'F' and resid 117 through 123 removed outlier: 4.224A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU F 169 " --> pdb=" O SER F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR F 192 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL F 193 " --> pdb=" O ASN F 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 189 through 193' Processing helix chain 'G' and resid 117 through 123 removed outlier: 4.136A pdb=" N LEU G 123 " --> pdb=" O VAL G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU G 169 " --> pdb=" O SER G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR G 192 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL G 193 " --> pdb=" O ASN G 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 189 through 193' Processing helix chain 'H' and resid 117 through 123 removed outlier: 4.168A pdb=" N LEU H 123 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU H 169 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR H 192 " --> pdb=" O GLU H 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL H 193 " --> pdb=" O ASN H 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 189 through 193' Processing helix chain 'I' and resid 117 through 123 removed outlier: 4.239A pdb=" N LEU I 123 " --> pdb=" O VAL I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 164 through 169 removed outlier: 3.781A pdb=" N LEU I 169 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR I 192 " --> pdb=" O GLU I 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL I 193 " --> pdb=" O ASN I 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 189 through 193' Processing helix chain 'J' and resid 117 through 123 removed outlier: 4.185A pdb=" N LEU J 123 " --> pdb=" O VAL J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU J 169 " --> pdb=" O SER J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 193 removed outlier: 4.154A pdb=" N TYR J 192 " --> pdb=" O GLU J 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL J 193 " --> pdb=" O ASN J 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 189 through 193' Processing helix chain 'K' and resid 117 through 123 removed outlier: 4.195A pdb=" N LEU K 123 " --> pdb=" O VAL K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 164 through 169 removed outlier: 3.781A pdb=" N LEU K 169 " --> pdb=" O SER K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR K 192 " --> pdb=" O GLU K 189 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL K 193 " --> pdb=" O ASN K 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 189 through 193' Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA A 212 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 108 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA A 185 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU A 110 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU A 183 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU A 112 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL A 181 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA A 198 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 201 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE A 126 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER A 146 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 128 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER A 144 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 130 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR A 142 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS A 132 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA B 212 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL B 108 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA B 185 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU B 110 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU B 183 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 112 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 181 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA B 198 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 201 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE B 126 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER B 146 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 128 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER B 144 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 130 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR B 142 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS B 132 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 65 through 66 removed outlier: 4.168A pdb=" N ALA C 212 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL C 108 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA C 185 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU C 110 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU C 183 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU C 112 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL C 181 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA C 198 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 201 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE C 126 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER C 146 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 128 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER C 144 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE C 130 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR C 142 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS C 132 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA D 212 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL D 108 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA D 185 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU D 110 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU D 183 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU D 112 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL D 181 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 90 removed outlier: 3.738A pdb=" N ALA D 198 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 201 " --> pdb=" O THR D 129 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE D 126 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER D 146 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL D 128 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER D 144 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE D 130 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR D 142 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS D 132 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA E 212 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL E 108 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA E 185 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU E 110 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU E 183 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU E 112 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL E 181 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA E 198 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU E 201 " --> pdb=" O THR E 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE E 126 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER E 146 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL E 128 " --> pdb=" O SER E 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER E 144 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE E 130 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR E 142 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS E 132 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA F 212 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL F 108 " --> pdb=" O ALA F 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA F 185 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU F 110 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU F 183 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU F 112 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL F 181 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA F 198 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU F 201 " --> pdb=" O THR F 129 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE F 126 " --> pdb=" O SER F 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER F 146 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL F 128 " --> pdb=" O SER F 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER F 144 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE F 130 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR F 142 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS F 132 " --> pdb=" O ILE F 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA G 212 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL G 108 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA G 185 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU G 110 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU G 183 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU G 112 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL G 181 " --> pdb=" O LEU G 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA G 198 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU G 201 " --> pdb=" O THR G 129 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE G 126 " --> pdb=" O SER G 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER G 146 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL G 128 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER G 144 " --> pdb=" O VAL G 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE G 130 " --> pdb=" O THR G 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR G 142 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS G 132 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA H 212 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL H 108 " --> pdb=" O ALA H 185 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA H 185 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU H 110 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU H 183 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU H 112 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL H 181 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 86 through 90 removed outlier: 3.738A pdb=" N ALA H 198 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU H 201 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE H 126 " --> pdb=" O SER H 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER H 146 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL H 128 " --> pdb=" O SER H 144 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER H 144 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE H 130 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR H 142 " --> pdb=" O ILE H 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS H 132 " --> pdb=" O ILE H 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA I 212 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL I 108 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA I 185 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU I 110 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU I 183 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU I 112 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL I 181 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA I 198 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU I 201 " --> pdb=" O THR I 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE I 126 " --> pdb=" O SER I 146 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER I 146 " --> pdb=" O PHE I 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL I 128 " --> pdb=" O SER I 144 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER I 144 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE I 130 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR I 142 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS I 132 " --> pdb=" O ILE I 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 65 through 66 removed outlier: 4.168A pdb=" N ALA J 212 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL J 108 " --> pdb=" O ALA J 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA J 185 " --> pdb=" O VAL J 108 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU J 110 " --> pdb=" O LEU J 183 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU J 183 " --> pdb=" O LEU J 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU J 112 " --> pdb=" O VAL J 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL J 181 " --> pdb=" O LEU J 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA J 198 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU J 201 " --> pdb=" O THR J 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE J 126 " --> pdb=" O SER J 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER J 146 " --> pdb=" O PHE J 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL J 128 " --> pdb=" O SER J 144 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER J 144 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE J 130 " --> pdb=" O THR J 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR J 142 " --> pdb=" O ILE J 130 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS J 132 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA K 212 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL K 108 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA K 185 " --> pdb=" O VAL K 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU K 110 " --> pdb=" O LEU K 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU K 183 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU K 112 " --> pdb=" O VAL K 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL K 181 " --> pdb=" O LEU K 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA K 198 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU K 201 " --> pdb=" O THR K 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE K 126 " --> pdb=" O SER K 146 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER K 146 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL K 128 " --> pdb=" O SER K 144 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER K 144 " --> pdb=" O VAL K 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE K 130 " --> pdb=" O THR K 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR K 142 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS K 132 " --> pdb=" O ILE K 140 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 825 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: 2.03 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4087 1.33 - 1.45: 2689 1.45 - 1.57: 7392 1.57 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 14267 Sorted by residual: bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.50e+00 ... (remaining 14262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 18318 2.54 - 5.09: 894 5.09 - 7.63: 83 7.63 - 10.18: 32 10.18 - 12.72: 66 Bond angle restraints: 19393 Sorted by residual: angle pdb=" N ASP G 122 " pdb=" CA ASP G 122 " pdb=" C ASP G 122 " ideal model delta sigma weight residual 111.07 120.94 -9.87 1.07e+00 8.73e-01 8.51e+01 angle pdb=" N ASP C 122 " pdb=" CA ASP C 122 " pdb=" C ASP C 122 " ideal model delta sigma weight residual 111.07 120.86 -9.79 1.07e+00 8.73e-01 8.38e+01 angle pdb=" N ASP F 122 " pdb=" CA ASP F 122 " pdb=" C ASP F 122 " ideal model delta sigma weight residual 111.07 120.83 -9.76 1.07e+00 8.73e-01 8.32e+01 angle pdb=" N ASP B 122 " pdb=" CA ASP B 122 " pdb=" C ASP B 122 " ideal model delta sigma weight residual 111.07 120.71 -9.64 1.07e+00 8.73e-01 8.11e+01 angle pdb=" N ASP A 122 " pdb=" CA ASP A 122 " pdb=" C ASP A 122 " ideal model delta sigma weight residual 111.07 120.64 -9.57 1.07e+00 8.73e-01 8.00e+01 ... (remaining 19388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 8011 22.27 - 44.55: 429 44.55 - 66.82: 41 66.82 - 89.10: 22 89.10 - 111.37: 275 Dihedral angle restraints: 8778 sinusoidal: 3619 harmonic: 5159 Sorted by residual: dihedral pdb=" CB CYS J 74 " pdb=" SG CYS J 74 " pdb=" SG CYS J 82 " pdb=" CB CYS J 82 " ideal model delta sinusoidal sigma weight residual 93.00 165.02 -72.02 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CB CYS K 74 " pdb=" SG CYS K 74 " pdb=" SG CYS K 82 " pdb=" CB CYS K 82 " ideal model delta sinusoidal sigma weight residual 93.00 165.01 -72.01 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CB CYS F 74 " pdb=" SG CYS F 74 " pdb=" SG CYS F 82 " pdb=" CB CYS F 82 " ideal model delta sinusoidal sigma weight residual 93.00 165.01 -72.01 1 1.00e+01 1.00e-02 6.63e+01 ... (remaining 8775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1569 0.057 - 0.113: 505 0.113 - 0.170: 138 0.170 - 0.226: 58 0.226 - 0.283: 40 Chirality restraints: 2310 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN F 88 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN I 88 " 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 1.99e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN K 88 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2307 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 114 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO H 115 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO H 115 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 115 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 114 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 115 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 114 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO C 115 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 115 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 115 " -0.031 5.00e-02 4.00e+02 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2816 2.77 - 3.30: 12393 3.30 - 3.83: 20325 3.83 - 4.37: 22644 4.37 - 4.90: 39722 Nonbonded interactions: 97900 Sorted by model distance: nonbonded pdb=" O THR I 134 " pdb=" OG1 THR I 196 " model vdw 2.235 3.040 nonbonded pdb=" O THR J 134 " pdb=" OG1 THR J 196 " model vdw 2.235 3.040 nonbonded pdb=" O THR K 134 " pdb=" OG1 THR K 196 " model vdw 2.235 3.040 nonbonded pdb=" O THR G 134 " pdb=" OG1 THR G 196 " model vdw 2.235 3.040 nonbonded pdb=" O THR B 134 " pdb=" OG1 THR B 196 " model vdw 2.235 3.040 ... (remaining 97895 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.120 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.011 0.055 14300 Z= 0.486 Angle : 1.403 12.722 19481 Z= 0.740 Chirality : 0.072 0.283 2310 Planarity : 0.008 0.055 2431 Dihedral : 26.681 111.373 5445 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % Rotamer: Outliers : 2.01 % Allowed : 11.30 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.69 (0.16), residues: 1738 helix: -2.40 (0.27), residues: 253 sheet: -3.81 (0.16), residues: 616 loop : -4.21 (0.16), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 71 TYR 0.021 0.004 TYR A 184 PHE 0.025 0.003 PHE J 126 HIS 0.007 0.003 HIS J 62 Details of bonding type rmsd covalent geometry : bond 0.01069 (14267) covalent geometry : angle 1.38336 (19393) SS BOND : bond 0.00354 ( 11) SS BOND : angle 0.24894 ( 22) hydrogen bonds : bond 0.23939 ( 297) hydrogen bonds : angle 8.93746 ( 825) link_BETA1-4 : bond 0.00239 ( 11) link_BETA1-4 : angle 4.90228 ( 33) link_NAG-ASN : bond 0.00513 ( 11) link_NAG-ASN : angle 3.63242 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 425 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 193 VAL cc_start: 0.8410 (p) cc_final: 0.8073 (m) REVERT: F 193 VAL cc_start: 0.8379 (p) cc_final: 0.8035 (m) REVERT: H 193 VAL cc_start: 0.8461 (p) cc_final: 0.8082 (m) REVERT: J 193 VAL cc_start: 0.8474 (p) cc_final: 0.8151 (m) outliers start: 30 outliers final: 15 residues processed: 444 average time/residue: 0.1225 time to fit residues: 77.5195 Evaluate side-chains 320 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 305 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain K residue 128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 120 ASN B 157 GLN C 120 ASN D 157 GLN E 120 ASN F 120 ASN F 157 GLN G 120 ASN ** G 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 ASN ** K 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105112 restraints weight = 19288.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.107624 restraints weight = 13008.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.109328 restraints weight = 10109.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110394 restraints weight = 8597.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111103 restraints weight = 7749.347| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14300 Z= 0.179 Angle : 0.893 11.747 19481 Z= 0.407 Chirality : 0.056 0.285 2310 Planarity : 0.006 0.046 2431 Dihedral : 30.309 100.630 2441 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 5.61 % Allowed : 20.12 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.17), residues: 1738 helix: -0.55 (0.33), residues: 187 sheet: -2.74 (0.18), residues: 660 loop : -3.82 (0.16), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 71 TYR 0.013 0.002 TYR A 69 PHE 0.008 0.001 PHE H 84 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00409 (14267) covalent geometry : angle 0.86707 (19393) SS BOND : bond 0.00630 ( 11) SS BOND : angle 2.80895 ( 22) hydrogen bonds : bond 0.05203 ( 297) hydrogen bonds : angle 5.91245 ( 825) link_BETA1-4 : bond 0.00363 ( 11) link_BETA1-4 : angle 3.45588 ( 33) link_NAG-ASN : bond 0.00288 ( 11) link_NAG-ASN : angle 3.48892 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 314 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 ASP cc_start: 0.7434 (p0) cc_final: 0.7157 (p0) REVERT: C 158 MET cc_start: 0.7379 (ttt) cc_final: 0.7153 (ttt) REVERT: G 75 ASP cc_start: 0.7409 (p0) cc_final: 0.7156 (p0) REVERT: I 75 ASP cc_start: 0.7490 (p0) cc_final: 0.7164 (p0) REVERT: I 125 MET cc_start: 0.7971 (mtt) cc_final: 0.7711 (mtt) REVERT: I 149 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8672 (tp) REVERT: I 158 MET cc_start: 0.7598 (ttm) cc_final: 0.7214 (ttt) REVERT: J 75 ASP cc_start: 0.7402 (p0) cc_final: 0.7171 (p0) REVERT: J 133 TYR cc_start: 0.8729 (p90) cc_final: 0.8464 (p90) REVERT: K 75 ASP cc_start: 0.7170 (p0) cc_final: 0.6910 (p0) outliers start: 84 outliers final: 56 residues processed: 362 average time/residue: 0.1096 time to fit residues: 57.9663 Evaluate side-chains 333 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 276 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 193 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 59 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 157 GLN B 120 ASN E 177 GLN F 120 ASN H 120 ASN J 120 ASN J 177 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111619 restraints weight = 19257.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114472 restraints weight = 12695.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116360 restraints weight = 9777.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.117585 restraints weight = 8292.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118280 restraints weight = 7471.560| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14300 Z= 0.204 Angle : 0.922 12.878 19481 Z= 0.404 Chirality : 0.052 0.256 2310 Planarity : 0.005 0.040 2431 Dihedral : 26.685 95.631 2434 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 7.22 % Allowed : 19.85 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.19), residues: 1738 helix: 0.16 (0.34), residues: 187 sheet: -2.10 (0.20), residues: 660 loop : -3.72 (0.17), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 206 TYR 0.018 0.002 TYR G 69 PHE 0.010 0.001 PHE D 126 HIS 0.005 0.001 HIS K 150 Details of bonding type rmsd covalent geometry : bond 0.00477 (14267) covalent geometry : angle 0.88500 (19393) SS BOND : bond 0.00275 ( 11) SS BOND : angle 3.22003 ( 22) hydrogen bonds : bond 0.04382 ( 297) hydrogen bonds : angle 5.42281 ( 825) link_BETA1-4 : bond 0.00371 ( 11) link_BETA1-4 : angle 3.57468 ( 33) link_NAG-ASN : bond 0.00319 ( 11) link_NAG-ASN : angle 4.69232 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 298 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7315 (p0) cc_final: 0.7073 (p0) REVERT: A 206 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.8192 (ptm-80) REVERT: B 112 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7674 (tt) REVERT: C 133 TYR cc_start: 0.8506 (p90) cc_final: 0.8300 (p90) REVERT: C 149 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8780 (tp) REVERT: C 158 MET cc_start: 0.7385 (ttt) cc_final: 0.7169 (ttt) REVERT: D 71 ARG cc_start: 0.7241 (ptp90) cc_final: 0.6951 (ttp-110) REVERT: D 112 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7630 (tt) REVERT: E 75 ASP cc_start: 0.7130 (p0) cc_final: 0.6920 (p0) REVERT: F 125 MET cc_start: 0.7941 (mtt) cc_final: 0.7485 (mtt) REVERT: H 120 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.8989 (t0) REVERT: H 149 LEU cc_start: 0.8948 (tm) cc_final: 0.8706 (tp) REVERT: H 209 LEU cc_start: 0.9094 (pp) cc_final: 0.8866 (pp) REVERT: I 125 MET cc_start: 0.7962 (mtt) cc_final: 0.7755 (mtt) REVERT: I 149 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8753 (tp) REVERT: K 112 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7529 (tt) REVERT: K 149 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8608 (tp) outliers start: 108 outliers final: 58 residues processed: 362 average time/residue: 0.1124 time to fit residues: 59.5234 Evaluate side-chains 341 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 276 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 120 ASN Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 216 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 193 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 70 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 120 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 57 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 157 optimal weight: 0.0570 chunk 95 optimal weight: 4.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN G 177 GLN H 120 ASN I 120 ASN I 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.143144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115266 restraints weight = 19190.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118293 restraints weight = 12199.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120322 restraints weight = 9221.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121471 restraints weight = 7751.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122389 restraints weight = 6978.536| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14300 Z= 0.135 Angle : 0.869 14.874 19481 Z= 0.369 Chirality : 0.050 0.251 2310 Planarity : 0.004 0.036 2431 Dihedral : 21.373 90.034 2431 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 5.35 % Allowed : 22.06 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.20), residues: 1738 helix: 0.85 (0.36), residues: 187 sheet: -1.75 (0.21), residues: 638 loop : -3.36 (0.18), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 206 TYR 0.019 0.001 TYR K 69 PHE 0.009 0.001 PHE B 84 HIS 0.005 0.001 HIS F 150 Details of bonding type rmsd covalent geometry : bond 0.00293 (14267) covalent geometry : angle 0.78058 (19393) SS BOND : bond 0.00344 ( 11) SS BOND : angle 2.94328 ( 22) hydrogen bonds : bond 0.03310 ( 297) hydrogen bonds : angle 5.20772 ( 825) link_BETA1-4 : bond 0.00282 ( 11) link_BETA1-4 : angle 4.22742 ( 33) link_NAG-ASN : bond 0.01242 ( 11) link_NAG-ASN : angle 7.98921 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 275 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.8064 (ptm-80) REVERT: B 112 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7532 (tt) REVERT: C 149 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8853 (tp) REVERT: C 158 MET cc_start: 0.7340 (ttt) cc_final: 0.7121 (ttt) REVERT: F 125 MET cc_start: 0.7730 (mtt) cc_final: 0.7494 (mtt) REVERT: H 149 LEU cc_start: 0.9035 (tm) cc_final: 0.8826 (tp) REVERT: I 149 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8790 (tp) REVERT: J 149 LEU cc_start: 0.8815 (tm) cc_final: 0.8594 (tp) REVERT: K 112 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7306 (tt) outliers start: 80 outliers final: 47 residues processed: 345 average time/residue: 0.1125 time to fit residues: 56.4325 Evaluate side-chains 300 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 249 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 193 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 127 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 168 optimal weight: 0.0670 chunk 4 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 219 HIS E 177 GLN I 177 GLN J 120 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.100955 restraints weight = 19400.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.103758 restraints weight = 12301.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105651 restraints weight = 9216.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.106854 restraints weight = 7667.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.107730 restraints weight = 6817.356| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14300 Z= 0.178 Angle : 0.800 9.817 19481 Z= 0.355 Chirality : 0.047 0.225 2310 Planarity : 0.004 0.041 2431 Dihedral : 18.394 83.278 2429 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 6.08 % Allowed : 21.59 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.19), residues: 1738 helix: 0.87 (0.36), residues: 198 sheet: -1.98 (0.20), residues: 660 loop : -3.39 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 206 TYR 0.019 0.001 TYR F 69 PHE 0.009 0.001 PHE H 172 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00414 (14267) covalent geometry : angle 0.75175 (19393) SS BOND : bond 0.00079 ( 11) SS BOND : angle 1.86076 ( 22) hydrogen bonds : bond 0.03609 ( 297) hydrogen bonds : angle 5.16773 ( 825) link_BETA1-4 : bond 0.00359 ( 11) link_BETA1-4 : angle 4.26018 ( 33) link_NAG-ASN : bond 0.00976 ( 11) link_NAG-ASN : angle 5.00655 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 260 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.8171 (ptm-80) REVERT: B 112 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7491 (tt) REVERT: C 149 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8994 (tp) REVERT: C 158 MET cc_start: 0.7394 (ttt) cc_final: 0.7175 (ttt) REVERT: F 125 MET cc_start: 0.7897 (mtt) cc_final: 0.7591 (mtt) REVERT: G 107 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8215 (tmt170) REVERT: G 122 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7803 (t0) REVERT: I 149 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8937 (tp) REVERT: J 133 TYR cc_start: 0.8579 (p90) cc_final: 0.8310 (p90) REVERT: K 112 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7294 (tt) outliers start: 91 outliers final: 59 residues processed: 324 average time/residue: 0.1237 time to fit residues: 57.4641 Evaluate side-chains 314 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 250 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 193 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 34 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN F 120 ASN F 177 GLN G 177 GLN I 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109584 restraints weight = 19006.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112484 restraints weight = 12176.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114437 restraints weight = 9157.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115667 restraints weight = 7650.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116514 restraints weight = 6831.615| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14300 Z= 0.134 Angle : 0.749 8.398 19481 Z= 0.329 Chirality : 0.046 0.307 2310 Planarity : 0.004 0.037 2431 Dihedral : 15.510 70.329 2429 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 5.75 % Allowed : 22.33 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.20), residues: 1738 helix: 1.60 (0.36), residues: 198 sheet: -1.83 (0.20), residues: 660 loop : -3.27 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 206 TYR 0.020 0.001 TYR E 69 PHE 0.007 0.001 PHE A 172 HIS 0.003 0.001 HIS G 217 Details of bonding type rmsd covalent geometry : bond 0.00301 (14267) covalent geometry : angle 0.71369 (19393) SS BOND : bond 0.00074 ( 11) SS BOND : angle 1.04540 ( 22) hydrogen bonds : bond 0.03006 ( 297) hydrogen bonds : angle 5.07877 ( 825) link_BETA1-4 : bond 0.00122 ( 11) link_BETA1-4 : angle 4.34319 ( 33) link_NAG-ASN : bond 0.00941 ( 11) link_NAG-ASN : angle 3.52598 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 241 time to evaluate : 0.510 Fit side-chains REVERT: A 206 ARG cc_start: 0.8439 (ttp-110) cc_final: 0.8167 (ptm-80) REVERT: B 112 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7345 (tt) REVERT: C 158 MET cc_start: 0.7339 (ttt) cc_final: 0.7137 (ttt) REVERT: G 122 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7756 (t0) REVERT: I 149 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9016 (tp) REVERT: K 112 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7214 (tt) outliers start: 86 outliers final: 65 residues processed: 299 average time/residue: 0.1251 time to fit residues: 52.8552 Evaluate side-chains 299 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 230 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 193 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 56 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 83 optimal weight: 8.9990 chunk 30 optimal weight: 0.0070 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 ASN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 GLN ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.105759 restraints weight = 19014.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108545 restraints weight = 12188.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110500 restraints weight = 9189.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111735 restraints weight = 7683.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112457 restraints weight = 6854.767| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14300 Z= 0.153 Angle : 0.757 9.630 19481 Z= 0.332 Chirality : 0.047 0.292 2310 Planarity : 0.004 0.037 2431 Dihedral : 13.182 55.752 2429 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 6.22 % Allowed : 21.46 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.20), residues: 1738 helix: 1.94 (0.36), residues: 198 sheet: -1.75 (0.20), residues: 660 loop : -3.20 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 206 TYR 0.017 0.001 TYR F 69 PHE 0.011 0.001 PHE F 172 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00353 (14267) covalent geometry : angle 0.71882 (19393) SS BOND : bond 0.00086 ( 11) SS BOND : angle 0.87239 ( 22) hydrogen bonds : bond 0.03133 ( 297) hydrogen bonds : angle 4.99477 ( 825) link_BETA1-4 : bond 0.00185 ( 11) link_BETA1-4 : angle 4.32989 ( 33) link_NAG-ASN : bond 0.00890 ( 11) link_NAG-ASN : angle 3.89484 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 243 time to evaluate : 0.412 Fit side-chains REVERT: A 206 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8216 (ptm-80) REVERT: B 112 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7353 (tt) REVERT: B 148 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8571 (ttp) REVERT: C 158 MET cc_start: 0.7385 (ttt) cc_final: 0.7153 (ttt) REVERT: G 122 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7739 (t0) REVERT: I 149 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8941 (tp) REVERT: I 177 GLN cc_start: 0.8437 (tt0) cc_final: 0.8231 (tp40) REVERT: J 133 TYR cc_start: 0.8692 (p90) cc_final: 0.8380 (p90) REVERT: K 112 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7255 (tt) outliers start: 93 outliers final: 71 residues processed: 310 average time/residue: 0.1222 time to fit residues: 54.1554 Evaluate side-chains 311 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 235 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 193 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 100 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 HIS B 177 GLN C 150 HIS C 177 GLN D 177 GLN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113358 restraints weight = 18751.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116292 restraints weight = 12034.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118267 restraints weight = 9103.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119344 restraints weight = 7654.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120269 restraints weight = 6908.552| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14300 Z= 0.110 Angle : 0.706 8.447 19481 Z= 0.313 Chirality : 0.044 0.236 2310 Planarity : 0.004 0.038 2431 Dihedral : 10.143 47.344 2429 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.15 % Allowed : 22.86 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.20), residues: 1738 helix: 1.90 (0.38), residues: 209 sheet: -1.68 (0.21), residues: 660 loop : -3.23 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 206 TYR 0.018 0.001 TYR F 69 PHE 0.013 0.001 PHE B 172 HIS 0.007 0.001 HIS G 150 Details of bonding type rmsd covalent geometry : bond 0.00233 (14267) covalent geometry : angle 0.66940 (19393) SS BOND : bond 0.00068 ( 11) SS BOND : angle 0.69515 ( 22) hydrogen bonds : bond 0.02408 ( 297) hydrogen bonds : angle 4.95123 ( 825) link_BETA1-4 : bond 0.00195 ( 11) link_BETA1-4 : angle 4.31007 ( 33) link_NAG-ASN : bond 0.00811 ( 11) link_NAG-ASN : angle 3.42183 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 236 time to evaluate : 0.554 Fit side-chains REVERT: B 112 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6957 (tt) REVERT: B 148 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8624 (ttp) REVERT: C 158 MET cc_start: 0.7313 (ttt) cc_final: 0.7069 (ttt) REVERT: I 149 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8909 (tp) REVERT: J 133 TYR cc_start: 0.8645 (p90) cc_final: 0.8316 (p90) REVERT: K 112 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7152 (tt) outliers start: 77 outliers final: 62 residues processed: 292 average time/residue: 0.1171 time to fit residues: 49.2080 Evaluate side-chains 291 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 216 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 123 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 168 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111877 restraints weight = 19013.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.114871 restraints weight = 12082.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.116828 restraints weight = 9073.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118049 restraints weight = 7604.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.118888 restraints weight = 6804.144| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14300 Z= 0.129 Angle : 0.683 9.324 19481 Z= 0.311 Chirality : 0.044 0.211 2310 Planarity : 0.004 0.045 2431 Dihedral : 8.124 43.940 2428 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 5.48 % Allowed : 22.53 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.21), residues: 1738 helix: 1.92 (0.37), residues: 209 sheet: -1.64 (0.21), residues: 660 loop : -3.15 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 206 TYR 0.020 0.001 TYR J 69 PHE 0.011 0.001 PHE B 172 HIS 0.006 0.001 HIS G 150 Details of bonding type rmsd covalent geometry : bond 0.00291 (14267) covalent geometry : angle 0.65091 (19393) SS BOND : bond 0.00117 ( 11) SS BOND : angle 0.71460 ( 22) hydrogen bonds : bond 0.02745 ( 297) hydrogen bonds : angle 4.80049 ( 825) link_BETA1-4 : bond 0.00199 ( 11) link_BETA1-4 : angle 3.95648 ( 33) link_NAG-ASN : bond 0.00615 ( 11) link_NAG-ASN : angle 3.21176 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 231 time to evaluate : 0.507 Fit side-chains REVERT: B 148 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8658 (ttp) REVERT: C 158 MET cc_start: 0.7345 (ttt) cc_final: 0.7122 (ttt) REVERT: I 149 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8890 (tp) REVERT: J 133 TYR cc_start: 0.8663 (p90) cc_final: 0.8438 (p90) REVERT: K 112 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7208 (tt) outliers start: 82 outliers final: 67 residues processed: 290 average time/residue: 0.1163 time to fit residues: 48.7792 Evaluate side-chains 297 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 227 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 121 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111562 restraints weight = 18807.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114439 restraints weight = 12101.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.116344 restraints weight = 9204.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117513 restraints weight = 7763.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118346 restraints weight = 6983.095| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14300 Z= 0.123 Angle : 0.658 8.605 19481 Z= 0.304 Chirality : 0.043 0.198 2310 Planarity : 0.004 0.045 2431 Dihedral : 7.337 39.084 2428 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 5.41 % Allowed : 22.86 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.21), residues: 1738 helix: 1.96 (0.37), residues: 209 sheet: -1.60 (0.21), residues: 660 loop : -3.15 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 206 TYR 0.019 0.001 TYR J 69 PHE 0.010 0.001 PHE B 172 HIS 0.013 0.001 HIS K 150 Details of bonding type rmsd covalent geometry : bond 0.00274 (14267) covalent geometry : angle 0.62929 (19393) SS BOND : bond 0.00149 ( 11) SS BOND : angle 0.78117 ( 22) hydrogen bonds : bond 0.02552 ( 297) hydrogen bonds : angle 4.80189 ( 825) link_BETA1-4 : bond 0.00096 ( 11) link_BETA1-4 : angle 3.67655 ( 33) link_NAG-ASN : bond 0.00628 ( 11) link_NAG-ASN : angle 3.05162 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 228 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7313 (tt) REVERT: B 148 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8684 (ttp) REVERT: C 158 MET cc_start: 0.7346 (ttt) cc_final: 0.7130 (ttt) REVERT: E 125 MET cc_start: 0.8143 (mmm) cc_final: 0.7682 (mtp) REVERT: I 149 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8861 (tp) REVERT: J 133 TYR cc_start: 0.8626 (p90) cc_final: 0.8399 (p90) REVERT: K 112 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7250 (tt) outliers start: 81 outliers final: 71 residues processed: 287 average time/residue: 0.1119 time to fit residues: 46.6110 Evaluate side-chains 296 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 221 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 174 GLU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 193 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 87 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 HIS ** J 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.140469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112679 restraints weight = 18745.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115478 restraints weight = 11950.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.117336 restraints weight = 9094.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118611 restraints weight = 7663.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119190 restraints weight = 6886.704| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14300 Z= 0.113 Angle : 0.642 8.226 19481 Z= 0.301 Chirality : 0.043 0.213 2310 Planarity : 0.004 0.046 2431 Dihedral : 6.662 36.680 2428 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.21 % Allowed : 23.40 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.21), residues: 1738 helix: 1.97 (0.37), residues: 209 sheet: -1.55 (0.21), residues: 660 loop : -3.13 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 206 TYR 0.020 0.001 TYR J 69 PHE 0.010 0.001 PHE B 172 HIS 0.016 0.001 HIS F 150 Details of bonding type rmsd covalent geometry : bond 0.00248 (14267) covalent geometry : angle 0.61635 (19393) SS BOND : bond 0.00053 ( 11) SS BOND : angle 0.73738 ( 22) hydrogen bonds : bond 0.02466 ( 297) hydrogen bonds : angle 4.75318 ( 825) link_BETA1-4 : bond 0.00102 ( 11) link_BETA1-4 : angle 3.21591 ( 33) link_NAG-ASN : bond 0.00587 ( 11) link_NAG-ASN : angle 3.06458 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.71 seconds wall clock time: 38 minutes 1.33 seconds (2281.33 seconds total)