Starting phenix.real_space_refine on Tue Jun 10 21:50:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uad_42060/06_2025/8uad_42060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uad_42060/06_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_42060/06_2025/8uad_42060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uad_42060/06_2025/8uad_42060.map" model { file = "/net/cci-nas-00/data/ceres_data/8uad_42060/06_2025/8uad_42060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uad_42060/06_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-5710/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: 7.66, per 1000 atoms: 0.62 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: 3.26 Conformation dependent library (CDL) restraints added in 2.1 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: 3.72 Time building geometry restraints manager: 3.80 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: 1.190 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.650 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.600 ------------------------------------------------------------------------------- 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 : 1.338 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: 1.4630 time to fit residues: 284.1904 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 : 1.322 ------------------------------------------------------------------------------- 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 = 0.126425 restraints weight = 12201.201| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.31 r_work: 0.3063 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 4.88711 ( 1314) SS BOND : bond 0.00320 ( 21) SS BOND : angle 1.14584 ( 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 : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8870 (mt0) cc_final: 0.8663 (mt0) REVERT: A 88 ARG cc_start: 0.7866 (ptt180) cc_final: 0.7516 (mtp-110) REVERT: B 59 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: C 75 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7653 (mptt) REVERT: C 88 ARG cc_start: 0.7874 (ptt180) cc_final: 0.7530 (mtp-110) REVERT: D 59 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: E 75 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8314 (mptt) REVERT: E 88 ARG cc_start: 0.7882 (ptt180) cc_final: 0.7490 (mtp-110) outliers start: 13 outliers final: 3 residues processed: 149 average time/residue: 1.3900 time to fit residues: 224.0445 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 : 1.248 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.3694 r_free = 0.3694 target = 0.157813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121451 restraints weight = 12467.803| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.13 r_work: 0.2992 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 12633 Z= 0.274 Angle : 0.892 9.937 17217 Z= 0.427 Chirality : 0.054 0.270 2064 Planarity : 0.006 0.044 2121 Dihedral : 12.408 79.348 2607 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: -0.38 (0.21), residues: 1521 helix: 1.21 (0.30), residues: 339 sheet: 0.27 (0.29), residues: 324 loop : -1.09 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 188 HIS 0.008 0.002 HIS E 99 PHE 0.017 0.003 PHE C 190 TYR 0.015 0.003 TYR E 307 ARG 0.004 0.001 ARG F 88 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 21) link_NAG-ASN : angle 1.83826 ( 63) link_BETA1-4 : bond 0.00714 ( 27) link_BETA1-4 : angle 2.24976 ( 81) hydrogen bonds : bond 0.07650 ( 468) hydrogen bonds : angle 4.89169 ( 1314) SS BOND : bond 0.00850 ( 21) SS BOND : angle 2.55285 ( 42) covalent geometry : bond 0.00678 (12564) covalent geometry : angle 0.86721 (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 : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8319 (tmtm) cc_final: 0.7730 (mptt) REVERT: A 88 ARG cc_start: 0.8072 (ptt180) cc_final: 0.7604 (mtp-110) REVERT: B 59 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: D 59 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: D 76 GLU cc_start: 0.8486 (mp0) cc_final: 0.8274 (mp0) REVERT: D 82 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: E 75 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8412 (mptt) REVERT: F 57 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7353 (pt0) outliers start: 25 outliers final: 11 residues processed: 159 average time/residue: 1.3625 time to fit residues: 234.0305 Evaluate side-chains 146 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.157092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120347 restraints weight = 12319.240| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.52 r_work: 0.2990 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12633 Z= 0.297 Angle : 0.924 10.127 17217 Z= 0.445 Chirality : 0.055 0.292 2064 Planarity : 0.007 0.060 2121 Dihedral : 10.632 67.927 2607 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.91 % Allowed : 12.50 % Favored : 84.59 % 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: -0.62 (0.21), residues: 1521 helix: 0.73 (0.29), residues: 357 sheet: 0.33 (0.28), residues: 339 loop : -1.29 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 188 HIS 0.008 0.002 HIS E 99 PHE 0.019 0.003 PHE C 190 TYR 0.016 0.003 TYR E 307 ARG 0.005 0.001 ARG A 335 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 21) link_NAG-ASN : angle 1.95628 ( 63) link_BETA1-4 : bond 0.00705 ( 27) link_BETA1-4 : angle 2.05615 ( 81) hydrogen bonds : bond 0.07934 ( 468) hydrogen bonds : angle 4.92354 ( 1314) SS BOND : bond 0.00855 ( 21) SS BOND : angle 2.59579 ( 42) covalent geometry : bond 0.00741 (12564) covalent geometry : angle 0.90135 (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: 37 poor density : 135 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8220 (tmtm) cc_final: 0.7680 (mptt) REVERT: B 59 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: B 132 GLU cc_start: 0.6859 (tt0) cc_final: 0.6382 (pm20) REVERT: D 59 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: D 82 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: E 75 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8448 (mptt) outliers start: 37 outliers final: 18 residues processed: 155 average time/residue: 1.2232 time to fit residues: 206.2298 Evaluate side-chains 156 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 143 CYS Chi-restraints excluded: chain A residue 146 ILE 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 10 SER 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 125 ILE 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: 8.9990 chunk 106 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 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: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.159777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.125051 restraints weight = 12279.839| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.09 r_work: 0.3021 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12633 Z= 0.177 Angle : 0.750 9.756 17217 Z= 0.358 Chirality : 0.047 0.265 2064 Planarity : 0.005 0.039 2121 Dihedral : 9.702 60.691 2607 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.28 % Allowed : 14.54 % Favored : 83.18 % 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: -0.38 (0.21), residues: 1521 helix: 1.09 (0.30), residues: 360 sheet: 0.45 (0.29), residues: 309 loop : -1.15 (0.19), residues: 852 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 0.001 ARG A 335 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 21) link_NAG-ASN : angle 1.74116 ( 63) link_BETA1-4 : bond 0.00722 ( 27) link_BETA1-4 : angle 1.91396 ( 81) hydrogen bonds : bond 0.06349 ( 468) hydrogen bonds : angle 4.81204 ( 1314) SS BOND : bond 0.00536 ( 21) SS BOND : angle 1.84941 ( 42) covalent geometry : bond 0.00423 (12564) covalent geometry : angle 0.72887 (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 166 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8237 (tmtm) cc_final: 0.7702 (mptt) REVERT: A 88 ARG cc_start: 0.8135 (ptt180) cc_final: 0.7698 (mtp-110) REVERT: A 265 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8604 (mt) REVERT: A 289 GLU cc_start: 0.8125 (tt0) cc_final: 0.7909 (mt-10) REVERT: B 59 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: B 132 GLU cc_start: 0.6864 (tt0) cc_final: 0.6400 (pm20) REVERT: C 75 LYS cc_start: 0.8118 (tptt) cc_final: 0.7777 (mptt) REVERT: D 59 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: E 75 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8459 (mptt) REVERT: F 132 GLU cc_start: 0.7274 (tt0) cc_final: 0.6733 (pm20) outliers start: 29 outliers final: 14 residues processed: 152 average time/residue: 1.2161 time to fit residues: 201.4818 Evaluate side-chains 162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 146 ILE 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 143 CYS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 58 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: 3.9990 chunk 105 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.159540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.121824 restraints weight = 12471.613| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.41 r_work: 0.3031 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.004 0.040 12633 Z= 0.187 Angle : 0.767 9.872 17217 Z= 0.365 Chirality : 0.048 0.268 2064 Planarity : 0.005 0.038 2121 Dihedral : 8.877 59.901 2607 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.59 % Allowed : 15.02 % Favored : 82.39 % 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: -0.35 (0.21), residues: 1521 helix: 1.20 (0.30), residues: 357 sheet: 0.22 (0.29), residues: 324 loop : -1.07 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 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 E 307 ARG 0.003 0.001 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 21) link_NAG-ASN : angle 1.71224 ( 63) link_BETA1-4 : bond 0.00742 ( 27) link_BETA1-4 : angle 1.94954 ( 81) hydrogen bonds : bond 0.06446 ( 468) hydrogen bonds : angle 4.77345 ( 1314) SS BOND : bond 0.00559 ( 21) SS BOND : angle 1.93936 ( 42) covalent geometry : bond 0.00448 (12564) covalent geometry : angle 0.74564 (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 184 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: A 75 LYS cc_start: 0.8210 (tmtm) cc_final: 0.7692 (mptt) REVERT: A 88 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7605 (mtp-110) REVERT: A 265 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8584 (mt) REVERT: A 289 GLU cc_start: 0.8092 (tt0) cc_final: 0.7874 (mt-10) REVERT: B 59 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: B 132 GLU cc_start: 0.6995 (tt0) cc_final: 0.6564 (pm20) REVERT: D 59 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: E 75 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8452 (mptt) REVERT: F 132 GLU cc_start: 0.7231 (tt0) cc_final: 0.6709 (pm20) outliers start: 33 outliers final: 18 residues processed: 170 average time/residue: 1.5267 time to fit residues: 282.0224 Evaluate side-chains 162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 48 GLU 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 340 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 47 LYS 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 324 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 58 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 340 LEU 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: 8.9990 chunk 115 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.160472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124180 restraints weight = 12242.924| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.26 r_work: 0.3020 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12633 Z= 0.166 Angle : 0.725 9.745 17217 Z= 0.345 Chirality : 0.046 0.266 2064 Planarity : 0.005 0.036 2121 Dihedral : 8.141 59.011 2607 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.52 % Allowed : 15.49 % Favored : 82.00 % 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: 1.26 (0.30), residues: 360 sheet: 0.22 (0.29), residues: 324 loop : -0.98 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 188 HIS 0.005 0.001 HIS E 294 PHE 0.016 0.002 PHE C 190 TYR 0.012 0.002 TYR A 307 ARG 0.002 0.000 ARG C 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 21) link_NAG-ASN : angle 1.66178 ( 63) link_BETA1-4 : bond 0.00749 ( 27) link_BETA1-4 : angle 1.97428 ( 81) hydrogen bonds : bond 0.06029 ( 468) hydrogen bonds : angle 4.73748 ( 1314) SS BOND : bond 0.00502 ( 21) SS BOND : angle 1.76102 ( 42) covalent geometry : bond 0.00395 (12564) covalent geometry : angle 0.70347 (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 177 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8241 (tmtm) cc_final: 0.7708 (mptt) REVERT: A 88 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7613 (mtp-110) REVERT: A 265 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8605 (mt) REVERT: A 289 GLU cc_start: 0.8100 (tt0) cc_final: 0.7888 (mt-10) REVERT: B 59 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8026 (mt-10) REVERT: B 132 GLU cc_start: 0.6977 (tt0) cc_final: 0.6532 (pm20) REVERT: C 75 LYS cc_start: 0.8135 (tptt) cc_final: 0.7829 (mptt) REVERT: C 323 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8409 (mtmm) REVERT: D 59 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8166 (mt-10) REVERT: E 75 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8469 (mptt) REVERT: F 132 GLU cc_start: 0.7198 (tt0) cc_final: 0.6702 (pm20) outliers start: 32 outliers final: 20 residues processed: 166 average time/residue: 1.3807 time to fit residues: 250.7567 Evaluate side-chains 168 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 170 LEU 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 323 LYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 58 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 146 ILE 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=2.00 ------------------------------------------------------------------------------- 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: 6.9990 chunk 11 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.163552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.127418 restraints weight = 12413.323| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.27 r_work: 0.3068 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12633 Z= 0.113 Angle : 0.621 9.592 17217 Z= 0.295 Chirality : 0.043 0.258 2064 Planarity : 0.004 0.035 2121 Dihedral : 7.307 57.415 2607 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.28 % Allowed : 15.88 % Favored : 81.84 % 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: 0.11 (0.21), residues: 1521 helix: 1.69 (0.30), residues: 357 sheet: 0.50 (0.29), residues: 309 loop : -0.81 (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 E 294 PHE 0.012 0.001 PHE C 190 TYR 0.009 0.001 TYR A 307 ARG 0.002 0.000 ARG B 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 21) link_NAG-ASN : angle 1.52724 ( 63) link_BETA1-4 : bond 0.00751 ( 27) link_BETA1-4 : angle 1.88806 ( 81) hydrogen bonds : bond 0.04735 ( 468) hydrogen bonds : angle 4.60199 ( 1314) SS BOND : bond 0.00322 ( 21) SS BOND : angle 1.22312 ( 42) covalent geometry : bond 0.00244 (12564) covalent geometry : angle 0.60025 (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 176 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8258 (tmtm) cc_final: 0.7699 (mptt) REVERT: A 88 ARG cc_start: 0.8069 (ptt180) cc_final: 0.7570 (mtp-110) REVERT: A 160 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8340 (t) REVERT: B 132 GLU cc_start: 0.6925 (tt0) cc_final: 0.6510 (pm20) REVERT: C 75 LYS cc_start: 0.8166 (tptt) cc_final: 0.7787 (mptt) REVERT: C 323 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8406 (mtmm) REVERT: D 132 GLU cc_start: 0.6928 (tt0) cc_final: 0.6651 (pm20) REVERT: E 75 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8420 (mptt) REVERT: E 160 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8407 (t) REVERT: F 98 LEU cc_start: 0.8604 (tp) cc_final: 0.8402 (tp) REVERT: F 132 GLU cc_start: 0.7158 (tt0) cc_final: 0.6677 (pm20) outliers start: 29 outliers final: 14 residues processed: 168 average time/residue: 1.1404 time to fit residues: 209.3984 Evaluate side-chains 159 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER 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 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 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: 0.9980 chunk 35 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 76 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.163793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125513 restraints weight = 12367.473| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.63 r_work: 0.3101 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12633 Z= 0.111 Angle : 0.614 9.631 17217 Z= 0.291 Chirality : 0.042 0.254 2064 Planarity : 0.004 0.036 2121 Dihedral : 7.007 57.889 2607 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.65 % Allowed : 17.22 % Favored : 81.13 % 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: 1.85 (0.30), residues: 357 sheet: 0.55 (0.29), residues: 309 loop : -0.73 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 271 HIS 0.003 0.001 HIS E 99 PHE 0.013 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 0.00313 ( 21) link_NAG-ASN : angle 1.47919 ( 63) link_BETA1-4 : bond 0.00752 ( 27) link_BETA1-4 : angle 1.83018 ( 81) hydrogen bonds : bond 0.04613 ( 468) hydrogen bonds : angle 4.53730 ( 1314) SS BOND : bond 0.00287 ( 21) SS BOND : angle 1.54259 ( 42) covalent geometry : bond 0.00241 (12564) covalent geometry : angle 0.59282 (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 162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8191 (tmtm) cc_final: 0.7714 (mptt) REVERT: A 88 ARG cc_start: 0.7991 (ptt180) cc_final: 0.7513 (mtp-110) REVERT: A 160 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8300 (t) REVERT: B 132 GLU cc_start: 0.6904 (tt0) cc_final: 0.6525 (pm20) REVERT: C 75 LYS cc_start: 0.8041 (tptt) cc_final: 0.7794 (mptt) REVERT: D 59 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7936 (mt-10) REVERT: D 132 GLU cc_start: 0.6880 (tt0) cc_final: 0.6660 (pm20) REVERT: F 125 MET cc_start: 0.7077 (ttp) cc_final: 0.6843 (ttp) REVERT: F 132 GLU cc_start: 0.7147 (tt0) cc_final: 0.6709 (pm20) outliers start: 21 outliers final: 15 residues processed: 155 average time/residue: 1.1642 time to fit residues: 197.3932 Evaluate side-chains 155 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 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 340 LEU 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 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 146 ILE 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: 0.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 0.0470 chunk 29 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.166839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.126345 restraints weight = 12463.154| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.96 r_work: 0.3155 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12633 Z= 0.107 Angle : 0.596 9.607 17217 Z= 0.284 Chirality : 0.042 0.252 2064 Planarity : 0.004 0.037 2121 Dihedral : 6.622 57.603 2607 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.42 % Allowed : 17.61 % Favored : 80.97 % 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 (0.22), residues: 1521 helix: 2.02 (0.30), residues: 357 sheet: 0.58 (0.30), residues: 309 loop : -0.63 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 158 HIS 0.004 0.001 HIS E 40 PHE 0.013 0.001 PHE C 190 TYR 0.009 0.001 TYR A 307 ARG 0.004 0.000 ARG B 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 21) link_NAG-ASN : angle 1.41229 ( 63) link_BETA1-4 : bond 0.00757 ( 27) link_BETA1-4 : angle 1.75150 ( 81) hydrogen bonds : bond 0.04378 ( 468) hydrogen bonds : angle 4.46024 ( 1314) SS BOND : bond 0.00338 ( 21) SS BOND : angle 1.78898 ( 42) covalent geometry : bond 0.00235 (12564) covalent geometry : angle 0.57401 (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 159 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.7971 (tmtm) cc_final: 0.7277 (mptt) REVERT: A 88 ARG cc_start: 0.7836 (ptt180) cc_final: 0.7126 (mtp-110) REVERT: A 160 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.7920 (t) REVERT: B 132 GLU cc_start: 0.6777 (tt0) cc_final: 0.6276 (pm20) REVERT: C 75 LYS cc_start: 0.7938 (tptt) cc_final: 0.7368 (mptt) REVERT: D 59 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7830 (mt-10) REVERT: D 132 GLU cc_start: 0.6824 (tt0) cc_final: 0.6497 (pm20) REVERT: F 59 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7817 (mt-10) REVERT: F 132 GLU cc_start: 0.7151 (tt0) cc_final: 0.6530 (pm20) outliers start: 18 outliers final: 16 residues processed: 154 average time/residue: 1.1382 time to fit residues: 192.0085 Evaluate side-chains 154 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER 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 142 SER 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 146 ILE 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: 3.9990 chunk 136 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.161456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.123550 restraints weight = 12331.030| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.89 r_work: 0.3058 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12633 Z= 0.156 Angle : 0.675 9.790 17217 Z= 0.323 Chirality : 0.045 0.260 2064 Planarity : 0.005 0.039 2121 Dihedral : 6.839 59.489 2607 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.73 % Allowed : 17.53 % Favored : 80.74 % 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: 0.21 (0.21), residues: 1521 helix: 1.74 (0.30), residues: 360 sheet: 0.57 (0.30), residues: 309 loop : -0.74 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 188 HIS 0.005 0.001 HIS A 99 PHE 0.015 0.002 PHE C 190 TYR 0.011 0.002 TYR A 307 ARG 0.003 0.001 ARG B 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 21) link_NAG-ASN : angle 1.48536 ( 63) link_BETA1-4 : bond 0.00754 ( 27) link_BETA1-4 : angle 1.73310 ( 81) hydrogen bonds : bond 0.05512 ( 468) hydrogen bonds : angle 4.56384 ( 1314) SS BOND : bond 0.00458 ( 21) SS BOND : angle 2.13697 ( 42) covalent geometry : bond 0.00372 (12564) covalent geometry : angle 0.65314 (17031) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9174.03 seconds wall clock time: 159 minutes 37.55 seconds (9577.55 seconds total)