Starting phenix.real_space_refine on Wed May 14 17:58:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uad_42060/05_2025/8uad_42060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uad_42060/05_2025/8uad_42060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uad_42060/05_2025/8uad_42060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uad_42060/05_2025/8uad_42060.map" model { file = "/net/cci-nas-00/data/ceres_data/8uad_42060/05_2025/8uad_42060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uad_42060/05_2025/8uad_42060.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.077 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 63 5.16 5 C 7722 2.51 5 N 2073 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12318 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2617 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 319} Chain: "B" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1277 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "C" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2617 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 319} Chain: "D" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1277 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "E" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2617 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 319} Chain: "F" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1277 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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: 7.14, per 1000 atoms: 0.58 Number of scatterers: 12318 At special positions: 0 Unit cell: (95.55, 93.73, 144.69, 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 63 16.00 O 2460 8.00 N 2073 7.00 C 7722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.05 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.02 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 272 " distance=2.04 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 318 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.05 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.02 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 272 " distance=2.04 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 318 " distance=2.04 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 57 " distance=2.05 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 143 " distance=2.02 Simple disulfide: pdb=" SG CYS E 178 " - pdb=" SG CYS E 272 " distance=2.04 Simple disulfide: pdb=" SG CYS E 292 " - pdb=" SG CYS E 318 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 401 " - " ASN A 59 " " NAG A 402 " - " ASN A 230 " " NAG C 401 " - " ASN C 59 " " NAG C 402 " - " ASN C 230 " " NAG E 401 " - " ASN E 59 " " NAG E 402 " - " ASN E 230 " " NAG G 1 " - " ASN A 330 " " NAG H 1 " - " ASN A 301 " " NAG I 1 " - " ASN A 25 " " NAG J 1 " - " ASN A 194 " " NAG K 1 " - " ASN A 145 " " NAG L 1 " - " ASN C 330 " " NAG M 1 " - " ASN C 301 " " NAG N 1 " - " ASN C 25 " " NAG O 1 " - " ASN C 194 " " NAG P 1 " - " ASN C 145 " " NAG Q 1 " - " ASN E 330 " " NAG R 1 " - " ASN E 301 " " NAG S 1 " - " ASN E 25 " " NAG T 1 " - " ASN E 194 " " NAG U 1 " - " ASN E 145 " Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 30 sheets defined 27.4% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.549A pdb=" N ARG A 101 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A 102 " --> pdb=" O HIS A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.527A pdb=" N GLY A 129 " --> pdb=" O ASN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.535A pdb=" N LYS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 removed outlier: 3.873A pdb=" N ILE B 6 " --> pdb=" O PHE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 57 removed outlier: 3.999A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 110 Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.532A pdb=" N LEU B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.518A pdb=" N GLU B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.550A pdb=" N ARG C 101 " --> pdb=" O MET C 98 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR C 102 " --> pdb=" O HIS C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 102' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.528A pdb=" N GLY C 129 " --> pdb=" O ASN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.536A pdb=" N LYS C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 removed outlier: 3.873A pdb=" N ILE D 6 " --> pdb=" O PHE D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 57 removed outlier: 3.999A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 110 Processing helix chain 'D' and resid 112 through 127 removed outlier: 3.532A pdb=" N LEU D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.518A pdb=" N GLU D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 68 Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.549A pdb=" N ARG E 101 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 102 " --> pdb=" O HIS E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 102' Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 126 through 130 removed outlier: 3.527A pdb=" N GLY E 129 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.536A pdb=" N LYS E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.873A pdb=" N ILE F 6 " --> pdb=" O PHE F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 57 removed outlier: 4.000A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 110 Processing helix chain 'F' and resid 112 through 127 removed outlier: 3.532A pdb=" N LEU F 118 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 158 through 163 removed outlier: 3.518A pdb=" N GLU F 161 " --> pdb=" O ASP F 158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.554A pdb=" N VAL B 131 " --> pdb=" O GLU B 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.102A pdb=" N ASN A 43 " --> pdb=" O ALA A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.527A pdb=" N ILE A 280 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 removed outlier: 7.494A pdb=" N VAL A 187 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE A 264 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AA8, first strand: chain 'A' and resid 170 through 174 Processing sheet with id=AA9, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AB1, first strand: chain 'A' and resid 306 through 307 Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 36 removed outlier: 3.555A pdb=" N VAL D 131 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.102A pdb=" N ASN C 43 " --> pdb=" O ALA C 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.527A pdb=" N ILE C 280 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 116 through 119 removed outlier: 7.494A pdb=" N VAL C 187 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE C 264 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AB9, first strand: chain 'C' and resid 170 through 174 Processing sheet with id=AC1, first strand: chain 'C' and resid 298 through 300 Processing sheet with id=AC2, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AC3, first strand: chain 'F' and resid 31 through 36 removed outlier: 3.556A pdb=" N VAL F 131 " --> pdb=" O GLU F 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AC6, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.102A pdb=" N ASN E 43 " --> pdb=" O ALA E 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 49 through 50 removed outlier: 3.527A pdb=" N ILE E 280 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 116 through 119 removed outlier: 7.493A pdb=" N VAL E 187 " --> pdb=" O PRO E 267 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE E 264 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 116 through 119 Processing sheet with id=AD1, first strand: chain 'E' and resid 170 through 174 Processing sheet with id=AD2, first strand: chain 'E' and resid 298 through 300 Processing sheet with id=AD3, first strand: chain 'E' and resid 306 through 307 492 hydrogen bonds defined for protein. 1314 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: 3.77 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3825 1.34 - 1.46: 2773 1.46 - 1.58: 5882 1.58 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 12564 Sorted by residual: bond pdb=" C1 BMA Q 3 " pdb=" C2 BMA Q 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C1 BMA L 3 " pdb=" C2 BMA L 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.79e+00 bond pdb=" C1 BMA S 3 " pdb=" C2 BMA S 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.78e+00 ... (remaining 12559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 16108 1.95 - 3.90: 724 3.90 - 5.85: 142 5.85 - 7.80: 45 7.80 - 9.75: 12 Bond angle restraints: 17031 Sorted by residual: angle pdb=" CA CYS C 94 " pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " ideal model delta sigma weight residual 114.40 124.15 -9.75 2.30e+00 1.89e-01 1.80e+01 angle pdb=" CA CYS A 94 " pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " ideal model delta sigma weight residual 114.40 124.14 -9.74 2.30e+00 1.89e-01 1.79e+01 angle pdb=" CA CYS E 94 " pdb=" CB CYS E 94 " pdb=" SG CYS E 94 " ideal model delta sigma weight residual 114.40 124.12 -9.72 2.30e+00 1.89e-01 1.79e+01 angle pdb=" C GLY C 93 " pdb=" N CYS C 94 " pdb=" CA CYS C 94 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C GLY A 93 " pdb=" N CYS A 94 " pdb=" CA CYS A 94 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 ... (remaining 17026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 7495 22.32 - 44.63: 449 44.63 - 66.95: 90 66.95 - 89.27: 81 89.27 - 111.59: 72 Dihedral angle restraints: 8187 sinusoidal: 3864 harmonic: 4323 Sorted by residual: dihedral pdb=" CA THR C 179 " pdb=" C THR C 179 " pdb=" N GLU C 180 " pdb=" CA GLU C 180 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA THR E 179 " pdb=" C THR E 179 " pdb=" N GLU E 180 " pdb=" CA GLU E 180 " ideal model delta harmonic sigma weight residual 180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA THR A 179 " pdb=" C THR A 179 " pdb=" N GLU A 180 " pdb=" CA GLU A 180 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1547 0.062 - 0.123: 426 0.123 - 0.185: 61 0.185 - 0.246: 12 0.246 - 0.308: 18 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CG LEU E 170 " pdb=" CB LEU E 170 " pdb=" CD1 LEU E 170 " pdb=" CD2 LEU E 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CG LEU A 170 " pdb=" CB LEU A 170 " pdb=" CD1 LEU A 170 " pdb=" CD2 LEU A 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CG LEU C 170 " pdb=" CB LEU C 170 " pdb=" CD1 LEU C 170 " pdb=" CD2 LEU C 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 2061 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 114 " 0.015 2.00e-02 2.50e+03 1.40e-02 3.41e+00 pdb=" CG PHE F 114 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE F 114 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE F 114 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 114 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 114 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 114 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 114 " 0.015 2.00e-02 2.50e+03 1.38e-02 3.35e+00 pdb=" CG PHE D 114 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 114 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 114 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 114 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 114 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 114 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 114 " -0.015 2.00e-02 2.50e+03 1.38e-02 3.33e+00 pdb=" CG PHE B 114 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 114 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 114 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 114 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 114 " -0.003 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1647 2.75 - 3.29: 10387 3.29 - 3.83: 18809 3.83 - 4.36: 22964 4.36 - 4.90: 41350 Nonbonded interactions: 95157 Sorted by model distance: nonbonded pdb=" OH TYR C 176 " pdb=" O GLU C 182 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR E 176 " pdb=" O GLU E 182 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 176 " pdb=" O GLU A 182 " model vdw 2.217 3.040 nonbonded pdb=" NZ LYS E 38 " pdb=" O SER E 39 " model vdw 2.221 3.120 nonbonded pdb=" NZ LYS C 38 " pdb=" O SER C 39 " model vdw 2.221 3.120 ... (remaining 95152 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'K' selection = chain 'P' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.770 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.009 0.057 12633 Z= 0.372 Angle : 1.044 9.749 17217 Z= 0.510 Chirality : 0.062 0.308 2064 Planarity : 0.006 0.042 2121 Dihedral : 20.425 111.586 5370 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.71 % Allowed : 0.94 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1521 helix: 0.35 (0.29), residues: 363 sheet: 0.45 (0.29), residues: 294 loop : -1.34 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 188 HIS 0.007 0.002 HIS C 294 PHE 0.033 0.003 PHE F 114 TYR 0.014 0.003 TYR A 307 ARG 0.008 0.001 ARG C 335 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 21) link_NAG-ASN : angle 2.08057 ( 63) link_BETA1-4 : bond 0.00794 ( 27) link_BETA1-4 : angle 2.04545 ( 81) hydrogen bonds : bond 0.15269 ( 468) hydrogen bonds : angle 5.62258 ( 1314) SS BOND : bond 0.00864 ( 21) SS BOND : angle 2.25091 ( 42) covalent geometry : bond 0.00899 (12564) covalent geometry : angle 1.02681 (17031) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 1.299 Fit side-chains REVERT: C 198 MET cc_start: 0.8819 (mmm) cc_final: 0.8521 (mmm) outliers start: 9 outliers final: 1 residues processed: 181 average time/residue: 1.4330 time to fit residues: 278.5574 Evaluate side-chains 111 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.163151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.126432 restraints weight = 12201.196| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.31 r_work: 0.3063 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12633 Z= 0.127 Angle : 0.710 9.261 17217 Z= 0.335 Chirality : 0.046 0.246 2064 Planarity : 0.005 0.037 2121 Dihedral : 15.607 87.895 2611 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.02 % Allowed : 7.70 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1521 helix: 1.50 (0.30), residues: 342 sheet: 0.57 (0.29), residues: 309 loop : -0.93 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 21 HIS 0.003 0.001 HIS E 99 PHE 0.014 0.002 PHE D 114 TYR 0.010 0.001 TYR A 307 ARG 0.003 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 21) link_NAG-ASN : angle 1.63383 ( 63) link_BETA1-4 : bond 0.00936 ( 27) link_BETA1-4 : angle 2.48624 ( 81) hydrogen bonds : bond 0.05458 ( 468) hydrogen bonds : angle 4.88712 ( 1314) SS BOND : bond 0.00320 ( 21) SS BOND : angle 1.14583 ( 42) covalent geometry : bond 0.00267 (12564) covalent geometry : angle 0.68325 (17031) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8872 (mt0) cc_final: 0.8664 (mt0) REVERT: A 88 ARG cc_start: 0.7865 (ptt180) cc_final: 0.7514 (mtp-110) REVERT: B 59 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: C 75 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7650 (mptt) REVERT: C 88 ARG cc_start: 0.7874 (ptt180) cc_final: 0.7530 (mtp-110) REVERT: D 59 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: E 75 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8313 (mptt) REVERT: E 88 ARG cc_start: 0.7883 (ptt180) cc_final: 0.7491 (mtp-110) outliers start: 13 outliers final: 3 residues processed: 149 average time/residue: 1.3235 time to fit residues: 213.7548 Evaluate side-chains 139 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.157551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.121663 restraints weight = 12468.309| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.02 r_work: 0.3003 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 12633 Z= 0.275 Angle : 0.897 9.956 17217 Z= 0.429 Chirality : 0.055 0.270 2064 Planarity : 0.006 0.046 2121 Dihedral : 12.408 79.393 2607 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.70 % Favored : 97.17 % Rotamer: Outliers : 1.97 % Allowed : 11.08 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1521 helix: 1.21 (0.30), residues: 339 sheet: 0.27 (0.29), residues: 324 loop : -1.10 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP E 188 HIS 0.008 0.002 HIS E 99 PHE 0.017 0.003 PHE C 190 TYR 0.016 0.003 TYR E 307 ARG 0.004 0.001 ARG E 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 21) link_NAG-ASN : angle 1.84429 ( 63) link_BETA1-4 : bond 0.00718 ( 27) link_BETA1-4 : angle 2.25665 ( 81) hydrogen bonds : bond 0.07722 ( 468) hydrogen bonds : angle 4.90135 ( 1314) SS BOND : bond 0.00781 ( 21) SS BOND : angle 2.60555 ( 42) covalent geometry : bond 0.00684 (12564) covalent geometry : angle 0.87202 (17031) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8319 (tmtm) cc_final: 0.7734 (mptt) REVERT: A 88 ARG cc_start: 0.8078 (ptt180) cc_final: 0.7593 (mtp-110) REVERT: B 59 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: D 59 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: D 76 GLU cc_start: 0.8490 (mp0) cc_final: 0.8279 (mp0) REVERT: D 82 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: E 75 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8410 (mptt) REVERT: F 57 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7343 (pt0) outliers start: 25 outliers final: 13 residues processed: 160 average time/residue: 1.2828 time to fit residues: 221.9987 Evaluate side-chains 147 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 96 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.156616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120834 restraints weight = 12287.407| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.06 r_work: 0.2975 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 12633 Z= 0.320 Angle : 0.958 10.251 17217 Z= 0.462 Chirality : 0.057 0.296 2064 Planarity : 0.007 0.067 2121 Dihedral : 10.727 68.142 2607 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.14 % Allowed : 12.66 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1521 helix: 0.65 (0.29), residues: 357 sheet: 0.32 (0.28), residues: 339 loop : -1.33 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 188 HIS 0.008 0.002 HIS E 99 PHE 0.022 0.003 PHE C 190 TYR 0.017 0.003 TYR E 307 ARG 0.006 0.001 ARG A 335 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 21) link_NAG-ASN : angle 2.00786 ( 63) link_BETA1-4 : bond 0.00718 ( 27) link_BETA1-4 : angle 2.09107 ( 81) hydrogen bonds : bond 0.08229 ( 468) hydrogen bonds : angle 4.94880 ( 1314) SS BOND : bond 0.00920 ( 21) SS BOND : angle 2.73903 ( 42) covalent geometry : bond 0.00801 (12564) covalent geometry : angle 0.93453 (17031) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8229 (tmtm) cc_final: 0.7715 (mptt) REVERT: B 59 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: B 132 GLU cc_start: 0.6882 (tt0) cc_final: 0.6423 (pm20) REVERT: D 59 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: D 82 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: E 75 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8464 (mptt) outliers start: 40 outliers final: 19 residues processed: 153 average time/residue: 1.1656 time to fit residues: 194.6993 Evaluate side-chains 155 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 24 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.161299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124986 restraints weight = 12242.558| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.26 r_work: 0.3028 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12633 Z= 0.143 Angle : 0.703 9.644 17217 Z= 0.335 Chirality : 0.045 0.261 2064 Planarity : 0.005 0.037 2121 Dihedral : 9.602 60.826 2607 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.73 % Allowed : 14.94 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1521 helix: 1.18 (0.30), residues: 360 sheet: 0.44 (0.29), residues: 309 loop : -1.09 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 188 HIS 0.004 0.001 HIS E 99 PHE 0.014 0.002 PHE C 190 TYR 0.011 0.001 TYR A 307 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 21) link_NAG-ASN : angle 1.71757 ( 63) link_BETA1-4 : bond 0.00729 ( 27) link_BETA1-4 : angle 1.89230 ( 81) hydrogen bonds : bond 0.05856 ( 468) hydrogen bonds : angle 4.79091 ( 1314) SS BOND : bond 0.00417 ( 21) SS BOND : angle 1.62682 ( 42) covalent geometry : bond 0.00327 (12564) covalent geometry : angle 0.68183 (17031) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8239 (tmtm) cc_final: 0.7696 (mptt) REVERT: A 88 ARG cc_start: 0.8128 (ptt180) cc_final: 0.7705 (mtp-110) REVERT: A 289 GLU cc_start: 0.8101 (tt0) cc_final: 0.7876 (mt-10) REVERT: B 59 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: B 132 GLU cc_start: 0.6911 (tt0) cc_final: 0.6416 (pm20) REVERT: C 75 LYS cc_start: 0.8100 (tptt) cc_final: 0.7768 (mptt) REVERT: D 59 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: E 75 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8432 (mptt) REVERT: F 132 GLU cc_start: 0.7270 (tt0) cc_final: 0.6725 (pm20) outliers start: 22 outliers final: 11 residues processed: 157 average time/residue: 1.1186 time to fit residues: 192.0235 Evaluate side-chains 151 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 143 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.158310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.122345 restraints weight = 12535.882| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.12 r_work: 0.3003 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12633 Z= 0.235 Angle : 0.834 10.029 17217 Z= 0.398 Chirality : 0.051 0.273 2064 Planarity : 0.006 0.041 2121 Dihedral : 9.296 59.690 2607 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.99 % Allowed : 14.39 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1521 helix: 1.08 (0.30), residues: 357 sheet: 0.24 (0.29), residues: 324 loop : -1.14 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 188 HIS 0.007 0.002 HIS E 99 PHE 0.018 0.002 PHE C 190 TYR 0.015 0.002 TYR E 307 ARG 0.003 0.001 ARG A 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 21) link_NAG-ASN : angle 1.80957 ( 63) link_BETA1-4 : bond 0.00730 ( 27) link_BETA1-4 : angle 1.97940 ( 81) hydrogen bonds : bond 0.07104 ( 468) hydrogen bonds : angle 4.82355 ( 1314) SS BOND : bond 0.00701 ( 21) SS BOND : angle 2.22950 ( 42) covalent geometry : bond 0.00577 (12564) covalent geometry : angle 0.81238 (17031) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8234 (tmtm) cc_final: 0.7719 (mptt) REVERT: A 88 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7588 (mtp-110) REVERT: A 265 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8607 (mt) REVERT: A 289 GLU cc_start: 0.8110 (tt0) cc_final: 0.7894 (mt-10) REVERT: B 59 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: B 132 GLU cc_start: 0.7005 (tt0) cc_final: 0.6574 (pm20) REVERT: D 59 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: E 75 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8474 (mptt) REVERT: F 132 GLU cc_start: 0.7256 (tt0) cc_final: 0.6724 (pm20) outliers start: 38 outliers final: 20 residues processed: 163 average time/residue: 1.1292 time to fit residues: 202.6883 Evaluate side-chains 173 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 8 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.160134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.123784 restraints weight = 12250.116| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.11 r_work: 0.3034 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12633 Z= 0.169 Angle : 0.737 9.754 17217 Z= 0.350 Chirality : 0.046 0.267 2064 Planarity : 0.005 0.037 2121 Dihedral : 8.537 59.539 2607 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.12 % Allowed : 15.41 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1521 helix: 1.28 (0.30), residues: 357 sheet: 0.45 (0.29), residues: 309 loop : -1.08 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 188 HIS 0.005 0.001 HIS E 99 PHE 0.017 0.002 PHE C 190 TYR 0.013 0.002 TYR A 307 ARG 0.002 0.000 ARG E 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 21) link_NAG-ASN : angle 1.71417 ( 63) link_BETA1-4 : bond 0.00743 ( 27) link_BETA1-4 : angle 1.95455 ( 81) hydrogen bonds : bond 0.06147 ( 468) hydrogen bonds : angle 4.75285 ( 1314) SS BOND : bond 0.00500 ( 21) SS BOND : angle 1.79152 ( 42) covalent geometry : bond 0.00403 (12564) covalent geometry : angle 0.71595 (17031) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8215 (tmtm) cc_final: 0.7689 (mptt) REVERT: A 88 ARG cc_start: 0.8109 (ptt180) cc_final: 0.7614 (mtp-110) REVERT: A 265 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8585 (mt) REVERT: A 289 GLU cc_start: 0.8072 (tt0) cc_final: 0.7865 (mt-10) REVERT: B 59 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: B 132 GLU cc_start: 0.6969 (tt0) cc_final: 0.6572 (pm20) REVERT: C 75 LYS cc_start: 0.8099 (tptt) cc_final: 0.7784 (mptt) REVERT: C 323 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8406 (mtmm) REVERT: D 59 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: E 75 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8465 (mptt) REVERT: F 132 GLU cc_start: 0.7212 (tt0) cc_final: 0.6701 (pm20) outliers start: 27 outliers final: 17 residues processed: 161 average time/residue: 1.1333 time to fit residues: 199.5012 Evaluate side-chains 158 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 84 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.162293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3331 r_free = 0.3331 target = 0.124942 restraints weight = 12408.146| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.49 r_work: 0.3061 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12633 Z= 0.126 Angle : 0.656 9.659 17217 Z= 0.311 Chirality : 0.044 0.259 2064 Planarity : 0.004 0.035 2121 Dihedral : 7.716 58.015 2607 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.36 % Allowed : 15.88 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1521 helix: 1.52 (0.30), residues: 360 sheet: 0.49 (0.29), residues: 309 loop : -0.91 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 14 HIS 0.004 0.001 HIS A 294 PHE 0.014 0.001 PHE C 190 TYR 0.010 0.001 TYR A 307 ARG 0.002 0.000 ARG B 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 21) link_NAG-ASN : angle 1.58308 ( 63) link_BETA1-4 : bond 0.00750 ( 27) link_BETA1-4 : angle 1.92162 ( 81) hydrogen bonds : bond 0.05196 ( 468) hydrogen bonds : angle 4.64670 ( 1314) SS BOND : bond 0.00367 ( 21) SS BOND : angle 1.38810 ( 42) covalent geometry : bond 0.00282 (12564) covalent geometry : angle 0.63496 (17031) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8246 (tmtm) cc_final: 0.7746 (mptt) REVERT: A 88 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7601 (mtp-110) REVERT: A 160 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8442 (t) REVERT: B 132 GLU cc_start: 0.6959 (tt0) cc_final: 0.6556 (pm20) REVERT: C 75 LYS cc_start: 0.8093 (tptt) cc_final: 0.7823 (mptt) REVERT: C 323 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8458 (mtmm) REVERT: D 132 GLU cc_start: 0.7029 (tt0) cc_final: 0.6635 (pm20) REVERT: E 75 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8452 (mptt) REVERT: E 160 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8459 (t) REVERT: F 132 GLU cc_start: 0.7159 (tt0) cc_final: 0.6692 (pm20) outliers start: 30 outliers final: 17 residues processed: 167 average time/residue: 1.1211 time to fit residues: 204.8097 Evaluate side-chains 163 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 0.0040 chunk 76 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN E 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.164583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127998 restraints weight = 12398.424| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.27 r_work: 0.3085 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12633 Z= 0.104 Angle : 0.602 9.605 17217 Z= 0.285 Chirality : 0.042 0.253 2064 Planarity : 0.004 0.038 2121 Dihedral : 7.116 57.222 2607 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.81 % Allowed : 16.98 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1521 helix: 1.89 (0.30), residues: 357 sheet: 0.56 (0.30), residues: 309 loop : -0.72 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 271 HIS 0.003 0.001 HIS C 220 PHE 0.011 0.001 PHE C 190 TYR 0.008 0.001 TYR A 307 ARG 0.002 0.000 ARG B 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 21) link_NAG-ASN : angle 1.47486 ( 63) link_BETA1-4 : bond 0.00753 ( 27) link_BETA1-4 : angle 1.85201 ( 81) hydrogen bonds : bond 0.04392 ( 468) hydrogen bonds : angle 4.52890 ( 1314) SS BOND : bond 0.00243 ( 21) SS BOND : angle 1.29682 ( 42) covalent geometry : bond 0.00216 (12564) covalent geometry : angle 0.58074 (17031) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8227 (tmtm) cc_final: 0.7688 (mptt) REVERT: A 88 ARG cc_start: 0.8043 (ptt180) cc_final: 0.7528 (mtp-110) REVERT: A 160 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8248 (t) REVERT: B 132 GLU cc_start: 0.6900 (tt0) cc_final: 0.6494 (pm20) REVERT: C 75 LYS cc_start: 0.8094 (tptt) cc_final: 0.7775 (mptt) REVERT: C 323 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8362 (mtmm) REVERT: D 132 GLU cc_start: 0.6961 (tt0) cc_final: 0.6611 (pm20) REVERT: F 132 GLU cc_start: 0.7154 (tt0) cc_final: 0.6575 (pm20) outliers start: 23 outliers final: 12 residues processed: 158 average time/residue: 1.1242 time to fit residues: 194.3692 Evaluate side-chains 149 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 114 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.0470 chunk 29 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.166662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126182 restraints weight = 12464.334| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.95 r_work: 0.3156 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12633 Z= 0.108 Angle : 0.606 9.629 17217 Z= 0.288 Chirality : 0.042 0.251 2064 Planarity : 0.004 0.037 2121 Dihedral : 6.780 57.929 2607 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.18 % Allowed : 17.92 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1521 helix: 2.02 (0.30), residues: 357 sheet: 0.62 (0.30), residues: 309 loop : -0.64 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 158 HIS 0.003 0.001 HIS A 220 PHE 0.012 0.001 PHE C 190 TYR 0.010 0.001 TYR A 307 ARG 0.003 0.000 ARG B 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 21) link_NAG-ASN : angle 1.41066 ( 63) link_BETA1-4 : bond 0.00762 ( 27) link_BETA1-4 : angle 1.78555 ( 81) hydrogen bonds : bond 0.04427 ( 468) hydrogen bonds : angle 4.45810 ( 1314) SS BOND : bond 0.00285 ( 21) SS BOND : angle 1.92274 ( 42) covalent geometry : bond 0.00236 (12564) covalent geometry : angle 0.58293 (17031) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8024 (tmtm) cc_final: 0.7332 (mptt) REVERT: A 88 ARG cc_start: 0.7894 (ptt180) cc_final: 0.7172 (mtp-110) REVERT: A 160 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.7934 (t) REVERT: B 132 GLU cc_start: 0.6804 (tt0) cc_final: 0.6341 (pm20) REVERT: C 75 LYS cc_start: 0.7924 (tptt) cc_final: 0.7429 (mptt) REVERT: D 59 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7905 (mt-10) REVERT: D 132 GLU cc_start: 0.6724 (tt0) cc_final: 0.6491 (pm20) REVERT: F 59 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7749 (mt-10) REVERT: F 132 GLU cc_start: 0.7079 (tt0) cc_final: 0.6427 (pm20) outliers start: 15 outliers final: 12 residues processed: 152 average time/residue: 1.1589 time to fit residues: 192.9515 Evaluate side-chains 153 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 106 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.163866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.122221 restraints weight = 12467.322| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.63 r_work: 0.3111 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12633 Z= 0.144 Angle : 0.666 9.736 17217 Z= 0.318 Chirality : 0.044 0.260 2064 Planarity : 0.005 0.040 2121 Dihedral : 6.849 59.245 2607 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.89 % Allowed : 17.45 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1521 helix: 1.79 (0.30), residues: 360 sheet: 0.59 (0.30), residues: 309 loop : -0.71 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 188 HIS 0.004 0.001 HIS A 99 PHE 0.014 0.002 PHE C 190 TYR 0.012 0.002 TYR A 307 ARG 0.003 0.000 ARG B 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 21) link_NAG-ASN : angle 1.48593 ( 63) link_BETA1-4 : bond 0.00764 ( 27) link_BETA1-4 : angle 1.76025 ( 81) hydrogen bonds : bond 0.05331 ( 468) hydrogen bonds : angle 4.55228 ( 1314) SS BOND : bond 0.00403 ( 21) SS BOND : angle 2.12446 ( 42) covalent geometry : bond 0.00337 (12564) covalent geometry : angle 0.64331 (17031) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8556.53 seconds wall clock time: 148 minutes 15.09 seconds (8895.09 seconds total)