Starting phenix.real_space_refine on Thu Jul 31 23:39:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ds5_8909/07_2025/6ds5_8909_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ds5_8909/07_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_8909/07_2025/6ds5_8909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ds5_8909/07_2025/6ds5_8909.map" model { file = "/net/cci-nas-00/data/ceres_data/6ds5_8909/07_2025/6ds5_8909_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ds5_8909/07_2025/6ds5_8909_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP: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: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP: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: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP: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: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP: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: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP: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: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP: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: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP: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: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP: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: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP: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: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP: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: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP: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: 8.48, per 1000 atoms: 0.61 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: 3.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.53 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: 3.48 Time building geometry restraints manager: 4.01 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' 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: 2.220 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.100 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.560 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.007 0.003 HIS J 62 PHE 0.025 0.003 PHE J 126 TYR 0.021 0.004 TYR A 184 ARG 0.007 0.001 ARG B 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 11) link_NAG-ASN : angle 3.63242 ( 33) link_BETA1-4 : bond 0.00239 ( 11) link_BETA1-4 : angle 4.90228 ( 33) hydrogen bonds : bond 0.23939 ( 297) hydrogen bonds : angle 8.93746 ( 825) SS BOND : bond 0.00354 ( 11) SS BOND : angle 0.24894 ( 22) covalent geometry : bond 0.01069 (14267) covalent geometry : angle 1.38336 (19393) *********************** 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 : 1.553 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: 0.2767 time to fit residues: 175.6175 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 : 1.660 ------------------------------------------------------------------------------- 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 148 optimal weight: 1.9990 chunk 133 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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** J 120 ASN ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109218 restraints weight = 19125.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111900 restraints weight = 12649.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.113726 restraints weight = 9724.705| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14300 Z= 0.154 Angle : 0.882 12.072 19481 Z= 0.398 Chirality : 0.057 0.297 2310 Planarity : 0.006 0.047 2431 Dihedral : 29.739 99.519 2441 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 6.15 % Allowed : 18.98 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.17), residues: 1738 helix: -0.46 (0.33), residues: 187 sheet: -2.69 (0.18), residues: 660 loop : -3.76 (0.17), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 150 PHE 0.011 0.001 PHE H 84 TYR 0.012 0.002 TYR H 133 ARG 0.005 0.001 ARG I 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 11) link_NAG-ASN : angle 3.58384 ( 33) link_BETA1-4 : bond 0.00108 ( 11) link_BETA1-4 : angle 3.37968 ( 33) hydrogen bonds : bond 0.04753 ( 297) hydrogen bonds : angle 5.92151 ( 825) SS BOND : bond 0.01629 ( 11) SS BOND : angle 2.80696 ( 22) covalent geometry : bond 0.00339 (14267) covalent geometry : angle 0.85502 (19393) *********************** 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 409 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 317 time to evaluate : 1.481 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: C 75 ASP cc_start: 0.7573 (p0) cc_final: 0.7302 (p0) REVERT: C 158 MET cc_start: 0.7385 (ttt) cc_final: 0.7157 (ttt) REVERT: E 149 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8488 (tp) REVERT: G 75 ASP cc_start: 0.7515 (p0) cc_final: 0.7244 (p0) REVERT: G 125 MET cc_start: 0.7899 (mtt) cc_final: 0.7378 (mtt) REVERT: I 75 ASP cc_start: 0.7659 (p0) cc_final: 0.7355 (p0) REVERT: I 125 MET cc_start: 0.7907 (mtt) cc_final: 0.7611 (mtt) REVERT: I 158 MET cc_start: 0.7561 (ttm) cc_final: 0.7173 (ttt) REVERT: J 75 ASP cc_start: 0.7541 (p0) cc_final: 0.7312 (p0) REVERT: J 133 TYR cc_start: 0.8717 (p90) cc_final: 0.8407 (p90) REVERT: K 75 ASP cc_start: 0.7294 (p0) cc_final: 0.7024 (p0) REVERT: K 149 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8503 (tp) outliers start: 92 outliers final: 58 residues processed: 372 average time/residue: 0.2371 time to fit residues: 129.8054 Evaluate side-chains 340 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 280 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 A residue 204 SER 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 193 VAL Chi-restraints excluded: chain B residue 204 SER 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 204 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 204 SER Chi-restraints excluded: chain D residue 206 ARG 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 E residue 204 SER 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 178 LEU Chi-restraints excluded: chain F residue 204 SER 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 G residue 204 SER 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 204 SER 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 193 VAL Chi-restraints excluded: chain I residue 204 SER 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 J residue 204 SER 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 Chi-restraints excluded: chain K residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 151 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 F 177 GLN ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.114624 restraints weight = 19173.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117502 restraints weight = 12515.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119437 restraints weight = 9585.837| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14300 Z= 0.147 Angle : 0.898 12.995 19481 Z= 0.388 Chirality : 0.052 0.257 2310 Planarity : 0.005 0.043 2431 Dihedral : 26.241 93.846 2434 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 6.22 % Allowed : 20.52 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.19), residues: 1738 helix: 0.55 (0.36), residues: 187 sheet: -2.06 (0.20), residues: 660 loop : -3.62 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 150 PHE 0.010 0.001 PHE I 126 TYR 0.019 0.001 TYR G 69 ARG 0.008 0.001 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 11) link_NAG-ASN : angle 4.53173 ( 33) link_BETA1-4 : bond 0.00336 ( 11) link_BETA1-4 : angle 3.78766 ( 33) hydrogen bonds : bond 0.03959 ( 297) hydrogen bonds : angle 5.43555 ( 825) SS BOND : bond 0.00247 ( 11) SS BOND : angle 3.39681 ( 22) covalent geometry : bond 0.00325 (14267) covalent geometry : angle 0.85855 (19393) *********************** 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 379 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 286 time to evaluate : 1.454 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: A 75 ASP cc_start: 0.7353 (p0) cc_final: 0.7082 (p0) REVERT: A 206 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.8112 (ptm-80) REVERT: B 112 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7356 (tt) REVERT: C 112 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7558 (tt) REVERT: C 149 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8628 (tp) REVERT: E 75 ASP cc_start: 0.7268 (p0) cc_final: 0.6997 (p0) REVERT: F 125 MET cc_start: 0.7776 (mtt) cc_final: 0.7366 (mtt) REVERT: G 148 MET cc_start: 0.8778 (tpp) cc_final: 0.8560 (ttt) REVERT: I 125 MET cc_start: 0.7804 (mtt) cc_final: 0.7590 (mtt) REVERT: J 149 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8663 (tp) REVERT: K 112 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7542 (tt) outliers start: 93 outliers final: 42 residues processed: 343 average time/residue: 0.2472 time to fit residues: 124.9103 Evaluate side-chains 308 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 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 178 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 149 LEU 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 162 LEU 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 193 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 178 LEU 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 162 LEU 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 140 ILE 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 193 VAL Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 149 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 5 optimal weight: 0.3980 chunk 166 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN F 120 ASN G 177 GLN I 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116229 restraints weight = 18937.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119210 restraints weight = 12081.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121198 restraints weight = 9143.718| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14300 Z= 0.140 Angle : 0.870 14.715 19481 Z= 0.370 Chirality : 0.049 0.244 2310 Planarity : 0.004 0.048 2431 Dihedral : 21.112 89.992 2430 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 5.48 % Allowed : 20.99 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.20), residues: 1738 helix: 0.80 (0.37), residues: 198 sheet: -1.80 (0.21), residues: 638 loop : -3.27 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 150 PHE 0.009 0.001 PHE B 126 TYR 0.021 0.001 TYR E 69 ARG 0.006 0.001 ARG I 71 Details of bonding type rmsd link_NAG-ASN : bond 0.01353 ( 11) link_NAG-ASN : angle 7.77749 ( 33) link_BETA1-4 : bond 0.00159 ( 11) link_BETA1-4 : angle 4.17636 ( 33) hydrogen bonds : bond 0.03310 ( 297) hydrogen bonds : angle 5.20395 ( 825) SS BOND : bond 0.01110 ( 11) SS BOND : angle 2.70614 ( 22) covalent geometry : bond 0.00311 (14267) covalent geometry : angle 0.78669 (19393) *********************** 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 328 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 246 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8598 (p90) cc_final: 0.8100 (p90) REVERT: A 206 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.8048 (ptm-80) REVERT: C 112 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7339 (tt) REVERT: C 149 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8661 (tp) REVERT: F 125 MET cc_start: 0.7737 (mtt) cc_final: 0.7456 (mtt) REVERT: J 149 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8655 (tp) REVERT: K 112 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7399 (tt) outliers start: 82 outliers final: 53 residues processed: 302 average time/residue: 0.3731 time to fit residues: 165.1315 Evaluate side-chains 292 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 142 THR Chi-restraints excluded: chain A residue 193 VAL 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 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 112 LEU 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 193 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 66 VAL 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 117 SER 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 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 140 ILE 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 112 LEU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 149 LEU 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 193 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN E 177 GLN F 120 ASN F 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 = 0.3415 r_free = 0.3415 target = 0.129755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.102028 restraints weight = 19144.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.104829 restraints weight = 12236.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.106732 restraints weight = 9198.970| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14300 Z= 0.167 Angle : 0.779 9.360 19481 Z= 0.345 Chirality : 0.047 0.372 2310 Planarity : 0.004 0.039 2431 Dihedral : 17.847 80.926 2429 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 6.68 % Allowed : 20.86 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.19), residues: 1738 helix: 1.11 (0.36), residues: 198 sheet: -1.99 (0.19), residues: 660 loop : -3.34 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 150 PHE 0.009 0.001 PHE B 172 TYR 0.020 0.001 TYR F 69 ARG 0.005 0.000 ARG E 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00873 ( 11) link_NAG-ASN : angle 4.71462 ( 33) link_BETA1-4 : bond 0.00221 ( 11) link_BETA1-4 : angle 4.37536 ( 33) hydrogen bonds : bond 0.03481 ( 297) hydrogen bonds : angle 5.17425 ( 825) SS BOND : bond 0.00106 ( 11) SS BOND : angle 1.98373 ( 22) covalent geometry : bond 0.00389 (14267) covalent geometry : angle 0.73122 (19393) *********************** 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 347 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 247 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8200 (ptm-80) REVERT: C 112 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7247 (tt) REVERT: C 149 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8842 (tp) REVERT: E 135 ARG cc_start: 0.7167 (mmt180) cc_final: 0.6944 (mmt180) REVERT: F 125 MET cc_start: 0.7856 (mtt) cc_final: 0.7594 (mtt) REVERT: G 122 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7757 (t0) REVERT: J 133 TYR cc_start: 0.8583 (p90) cc_final: 0.8309 (p90) REVERT: J 149 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8755 (tp) REVERT: K 112 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7289 (tt) outliers start: 100 outliers final: 68 residues processed: 312 average time/residue: 0.2688 time to fit residues: 122.2578 Evaluate side-chains 312 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 239 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 142 THR Chi-restraints excluded: chain A residue 181 VAL 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 142 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 112 LEU 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 142 THR Chi-restraints excluded: chain D residue 162 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 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 190 ASN 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 117 SER 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 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 128 VAL Chi-restraints excluded: chain H residue 139 ILE 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 112 LEU Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 142 THR 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 149 LEU 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 142 THR 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 132 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN F 177 GLN H 219 HIS I 177 GLN I 219 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.136765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109126 restraints weight = 19115.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111850 restraints weight = 12281.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113701 restraints weight = 9326.151| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14300 Z= 0.156 Angle : 0.757 9.480 19481 Z= 0.335 Chirality : 0.047 0.280 2310 Planarity : 0.004 0.036 2431 Dihedral : 15.289 69.281 2429 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 6.89 % Allowed : 21.66 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.20), residues: 1738 helix: 1.42 (0.36), residues: 198 sheet: -1.89 (0.20), residues: 660 loop : -3.26 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 217 PHE 0.010 0.001 PHE A 172 TYR 0.017 0.001 TYR E 69 ARG 0.007 0.001 ARG J 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 11) link_NAG-ASN : angle 3.46693 ( 33) link_BETA1-4 : bond 0.00096 ( 11) link_BETA1-4 : angle 4.38092 ( 33) hydrogen bonds : bond 0.03197 ( 297) hydrogen bonds : angle 5.05016 ( 825) SS BOND : bond 0.00454 ( 11) SS BOND : angle 1.10805 ( 22) covalent geometry : bond 0.00361 (14267) covalent geometry : angle 0.72164 (19393) *********************** 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 339 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 236 time to evaluate : 2.975 Fit side-chains REVERT: A 69 TYR cc_start: 0.8573 (p90) cc_final: 0.8097 (p90) REVERT: A 206 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.8189 (ptm-80) REVERT: C 112 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.6936 (tt) REVERT: D 148 MET cc_start: 0.8726 (tpp) cc_final: 0.8480 (ttt) REVERT: E 148 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8233 (ttp) REVERT: K 112 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7263 (tt) outliers start: 103 outliers final: 76 residues processed: 305 average time/residue: 0.3064 time to fit residues: 135.8355 Evaluate side-chains 305 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 226 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 117 SER 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 C residue 66 VAL Chi-restraints excluded: chain C residue 112 LEU 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 162 LEU 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 112 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 148 MET 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 117 SER 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 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 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 142 THR Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 86 VAL 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 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 193 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 140 optimal weight: 0.0980 chunk 143 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 ASN ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN I 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109228 restraints weight = 19032.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112087 restraints weight = 12203.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.113954 restraints weight = 9238.483| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4093 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= 0.128 Angle : 0.727 10.995 19481 Z= 0.320 Chirality : 0.046 0.227 2310 Planarity : 0.004 0.040 2431 Dihedral : 11.453 58.133 2429 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.75 % Allowed : 21.06 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.20), residues: 1738 helix: 1.48 (0.37), residues: 209 sheet: -1.82 (0.20), residues: 660 loop : -3.27 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 219 PHE 0.016 0.001 PHE F 172 TYR 0.020 0.001 TYR G 69 ARG 0.007 0.001 ARG G 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 11) link_NAG-ASN : angle 3.38026 ( 33) link_BETA1-4 : bond 0.00146 ( 11) link_BETA1-4 : angle 4.41640 ( 33) hydrogen bonds : bond 0.02787 ( 297) hydrogen bonds : angle 4.99674 ( 825) SS BOND : bond 0.00177 ( 11) SS BOND : angle 0.98527 ( 22) covalent geometry : bond 0.00286 (14267) covalent geometry : angle 0.69072 (19393) *********************** 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 338 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 237 time to evaluate : 1.823 Fit side-chains REVERT: A 148 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8428 (ttp) REVERT: A 206 ARG cc_start: 0.8349 (ttp-110) cc_final: 0.8145 (ptm-80) REVERT: C 112 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7390 (tt) REVERT: D 135 ARG cc_start: 0.7211 (mmt180) cc_final: 0.6745 (mmt180) REVERT: G 69 TYR cc_start: 0.8414 (p90) cc_final: 0.7919 (p90) REVERT: K 112 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7246 (tt) REVERT: K 148 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8539 (ttp) outliers start: 101 outliers final: 71 residues processed: 309 average time/residue: 0.3766 time to fit residues: 166.2380 Evaluate side-chains 302 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 227 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 148 MET 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 117 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 139 ILE 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 C residue 66 VAL Chi-restraints excluded: chain C residue 112 LEU 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 193 VAL Chi-restraints excluded: chain D residue 86 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 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 117 SER 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 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 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 142 THR 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 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 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 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 148 MET 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 21 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 HIS C 177 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 177 GLN G 219 HIS ** K 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.131259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.103006 restraints weight = 19087.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.105738 restraints weight = 12477.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.107490 restraints weight = 9557.018| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14300 Z= 0.218 Angle : 0.765 9.123 19481 Z= 0.347 Chirality : 0.046 0.203 2310 Planarity : 0.004 0.041 2431 Dihedral : 9.456 43.711 2429 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 6.89 % Allowed : 21.32 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.20), residues: 1738 helix: 1.68 (0.35), residues: 198 sheet: -1.87 (0.20), residues: 660 loop : -3.15 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 150 PHE 0.010 0.001 PHE A 172 TYR 0.016 0.002 TYR F 69 ARG 0.007 0.001 ARG D 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 11) link_NAG-ASN : angle 3.87869 ( 33) link_BETA1-4 : bond 0.00272 ( 11) link_BETA1-4 : angle 4.17445 ( 33) hydrogen bonds : bond 0.03481 ( 297) hydrogen bonds : angle 4.84423 ( 825) SS BOND : bond 0.00202 ( 11) SS BOND : angle 0.88719 ( 22) covalent geometry : bond 0.00516 (14267) covalent geometry : angle 0.72886 (19393) *********************** 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 352 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 249 time to evaluate : 1.560 Fit side-chains REVERT: A 148 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8576 (ttp) REVERT: E 125 MET cc_start: 0.8194 (mmm) cc_final: 0.7947 (mtp) REVERT: G 107 ARG cc_start: 0.8657 (ttt-90) cc_final: 0.8390 (tmt170) REVERT: G 219 HIS cc_start: 0.6914 (OUTLIER) cc_final: 0.6683 (m-70) REVERT: H 176 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8231 (mtmm) REVERT: J 133 TYR cc_start: 0.8740 (p90) cc_final: 0.8430 (p90) REVERT: K 112 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7278 (tt) outliers start: 103 outliers final: 80 residues processed: 325 average time/residue: 0.3302 time to fit residues: 151.6853 Evaluate side-chains 323 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 240 time to evaluate : 4.905 ------------------------------------------------------------------------------- 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 148 MET 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 117 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 139 ILE 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 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 181 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 139 ILE 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 E residue 66 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 122 ASP 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 117 SER 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 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 G residue 219 HIS 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 142 THR 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 86 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 193 VAL Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 122 ASP 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 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 178 LEU Chi-restraints excluded: chain K residue 193 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 4 optimal weight: 0.0040 chunk 25 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN ** G 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 HIS ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 GLN ** 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 = 0.3539 r_free = 0.3539 target = 0.138369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110195 restraints weight = 18846.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113044 restraints weight = 12259.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.114929 restraints weight = 9362.443| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.003 0.021 14300 Z= 0.116 Angle : 0.684 8.459 19481 Z= 0.314 Chirality : 0.044 0.240 2310 Planarity : 0.004 0.047 2431 Dihedral : 8.130 39.243 2429 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 5.28 % Allowed : 22.53 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.21), residues: 1738 helix: 2.11 (0.36), residues: 198 sheet: -1.74 (0.21), residues: 660 loop : -3.08 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS G 219 PHE 0.012 0.001 PHE H 172 TYR 0.018 0.001 TYR F 69 ARG 0.007 0.001 ARG I 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 11) link_NAG-ASN : angle 2.95435 ( 33) link_BETA1-4 : bond 0.00083 ( 11) link_BETA1-4 : angle 3.98706 ( 33) hydrogen bonds : bond 0.02698 ( 297) hydrogen bonds : angle 4.91505 ( 825) SS BOND : bond 0.00290 ( 11) SS BOND : angle 0.80977 ( 22) covalent geometry : bond 0.00254 (14267) covalent geometry : angle 0.65339 (19393) *********************** 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 315 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 236 time to evaluate : 2.228 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8537 (ttp) REVERT: B 122 ASP cc_start: 0.8007 (t0) cc_final: 0.7729 (t0) REVERT: C 135 ARG cc_start: 0.7265 (mmt180) cc_final: 0.6859 (mmt180) REVERT: G 219 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.6669 (m170) REVERT: J 133 TYR cc_start: 0.8697 (p90) cc_final: 0.8449 (p90) REVERT: K 112 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7137 (tt) outliers start: 79 outliers final: 72 residues processed: 296 average time/residue: 0.3490 time to fit residues: 146.7675 Evaluate side-chains 303 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 228 time to evaluate : 3.974 ------------------------------------------------------------------------------- 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 148 MET Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 THR 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 139 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 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 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 F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 117 SER 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 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 G residue 219 HIS 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 142 THR Chi-restraints excluded: chain H residue 160 ASP 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 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 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 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 114 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 141 optimal weight: 0.0050 chunk 99 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 HIS H 177 GLN ** K 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108984 restraints weight = 18904.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111814 restraints weight = 12268.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113592 restraints weight = 9362.195| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14300 Z= 0.125 Angle : 0.665 8.482 19481 Z= 0.309 Chirality : 0.044 0.204 2310 Planarity : 0.004 0.049 2431 Dihedral : 7.467 37.727 2429 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 5.41 % Allowed : 22.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.21), residues: 1738 helix: 1.78 (0.37), residues: 209 sheet: -1.67 (0.21), residues: 660 loop : -3.20 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS G 219 PHE 0.012 0.001 PHE A 172 TYR 0.018 0.001 TYR F 69 ARG 0.008 0.001 ARG F 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 11) link_NAG-ASN : angle 2.91450 ( 33) link_BETA1-4 : bond 0.00056 ( 11) link_BETA1-4 : angle 3.65659 ( 33) hydrogen bonds : bond 0.02715 ( 297) hydrogen bonds : angle 4.83390 ( 825) SS BOND : bond 0.00029 ( 11) SS BOND : angle 0.72410 ( 22) covalent geometry : bond 0.00280 (14267) covalent geometry : angle 0.63739 (19393) ********************** 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 313 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 232 time to evaluate : 1.715 Fit side-chains REVERT: A 148 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8580 (ttp) REVERT: B 122 ASP cc_start: 0.8033 (t0) cc_final: 0.7750 (t0) REVERT: C 135 ARG cc_start: 0.7291 (mmt180) cc_final: 0.6944 (mmt180) REVERT: J 133 TYR cc_start: 0.8709 (p90) cc_final: 0.8415 (p90) REVERT: K 112 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7191 (tt) outliers start: 81 outliers final: 75 residues processed: 293 average time/residue: 0.4245 time to fit residues: 178.2782 Evaluate side-chains 304 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 227 time to evaluate : 2.634 ------------------------------------------------------------------------------- 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 148 MET Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 162 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 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 F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 117 SER 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 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 142 THR Chi-restraints excluded: chain H residue 160 ASP 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 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 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 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 100 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109342 restraints weight = 18903.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.112179 restraints weight = 12267.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114071 restraints weight = 9372.537| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14300 Z= 0.124 Angle : 0.648 8.444 19481 Z= 0.305 Chirality : 0.043 0.218 2310 Planarity : 0.004 0.047 2431 Dihedral : 6.630 35.761 2429 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.68 % Allowed : 22.53 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.21), residues: 1738 helix: 1.82 (0.37), residues: 209 sheet: -1.64 (0.21), residues: 660 loop : -3.17 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS J 150 PHE 0.013 0.001 PHE A 172 TYR 0.018 0.001 TYR F 69 ARG 0.008 0.001 ARG J 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 11) link_NAG-ASN : angle 3.01843 ( 33) link_BETA1-4 : bond 0.00113 ( 11) link_BETA1-4 : angle 3.07720 ( 33) hydrogen bonds : bond 0.02599 ( 297) hydrogen bonds : angle 4.79606 ( 825) SS BOND : bond 0.00038 ( 11) SS BOND : angle 0.70592 ( 22) covalent geometry : bond 0.00281 (14267) covalent geometry : angle 0.62377 (19393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5146.11 seconds wall clock time: 96 minutes 58.91 seconds (5818.91 seconds total)