Starting phenix.real_space_refine on Mon May 19 20:57:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yd2_39163/05_2025/8yd2_39163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yd2_39163/05_2025/8yd2_39163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yd2_39163/05_2025/8yd2_39163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yd2_39163/05_2025/8yd2_39163.map" model { file = "/net/cci-nas-00/data/ceres_data/8yd2_39163/05_2025/8yd2_39163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yd2_39163/05_2025/8yd2_39163.cif" } resolution = 2.39 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= 0.002 sd= 0.067 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: 5 Type Number sf(0) Gaussians S 119 5.16 5 B 14 2.79 5 C 12334 2.51 5 N 3325 2.21 5 O 3780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19572 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "C" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "D" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "E" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "F" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "G" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "H" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "I" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "J" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "K" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "L" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "M" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "N" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.04, per 1000 atoms: 0.56 Number of scatterers: 19572 At special positions: 0 Unit cell: (110.05, 108.63, 103.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 O 3780 8.00 N 3325 7.00 C 12334 6.00 B 14 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 2.6 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 35 sheets defined 54.5% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 37 through 55 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 133 through 159 Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 49 through 67 Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 147 through 173 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 37 through 55 Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 133 through 159 Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 49 through 67 Processing helix chain 'D' and resid 82 through 96 Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 147 through 173 Processing helix chain 'D' and resid 175 through 183 Processing helix chain 'D' and resid 190 through 197 Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 37 through 55 Processing helix chain 'E' and resid 70 through 84 Processing helix chain 'E' and resid 98 through 106 Processing helix chain 'E' and resid 133 through 159 Processing helix chain 'E' and resid 161 through 169 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'F' and resid 32 through 39 Processing helix chain 'F' and resid 49 through 67 Processing helix chain 'F' and resid 82 through 96 Processing helix chain 'F' and resid 110 through 118 Processing helix chain 'F' and resid 147 through 173 Processing helix chain 'F' and resid 175 through 183 Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 37 through 55 Processing helix chain 'G' and resid 70 through 84 Processing helix chain 'G' and resid 98 through 106 Processing helix chain 'G' and resid 133 through 159 Processing helix chain 'G' and resid 161 through 169 Processing helix chain 'G' and resid 176 through 184 Processing helix chain 'H' and resid 32 through 39 Processing helix chain 'H' and resid 49 through 67 Processing helix chain 'H' and resid 82 through 96 Processing helix chain 'H' and resid 110 through 118 Processing helix chain 'H' and resid 147 through 173 Processing helix chain 'H' and resid 175 through 183 Processing helix chain 'H' and resid 190 through 197 Processing helix chain 'I' and resid 16 through 27 Processing helix chain 'I' and resid 37 through 55 Processing helix chain 'I' and resid 70 through 84 Processing helix chain 'I' and resid 98 through 106 Processing helix chain 'I' and resid 133 through 159 Processing helix chain 'I' and resid 161 through 169 Processing helix chain 'I' and resid 176 through 184 Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 49 through 67 Processing helix chain 'J' and resid 82 through 96 Processing helix chain 'J' and resid 110 through 118 Processing helix chain 'J' and resid 147 through 173 Processing helix chain 'J' and resid 175 through 183 Processing helix chain 'J' and resid 190 through 197 Processing helix chain 'K' and resid 16 through 27 Processing helix chain 'K' and resid 37 through 55 Processing helix chain 'K' and resid 70 through 84 Processing helix chain 'K' and resid 98 through 106 Processing helix chain 'K' and resid 133 through 159 Processing helix chain 'K' and resid 161 through 169 Processing helix chain 'K' and resid 176 through 184 Processing helix chain 'L' and resid 32 through 39 Processing helix chain 'L' and resid 49 through 67 Processing helix chain 'L' and resid 82 through 96 Processing helix chain 'L' and resid 110 through 118 Processing helix chain 'L' and resid 147 through 173 Processing helix chain 'L' and resid 175 through 183 Processing helix chain 'L' and resid 190 through 197 Processing helix chain 'M' and resid 16 through 27 Processing helix chain 'M' and resid 37 through 55 Processing helix chain 'M' and resid 70 through 84 Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 133 through 159 Processing helix chain 'M' and resid 161 through 169 Processing helix chain 'M' and resid 176 through 184 Processing helix chain 'N' and resid 32 through 39 Processing helix chain 'N' and resid 49 through 67 Processing helix chain 'N' and resid 82 through 96 Processing helix chain 'N' and resid 110 through 118 Processing helix chain 'N' and resid 147 through 173 Processing helix chain 'N' and resid 175 through 183 Processing helix chain 'N' and resid 190 through 197 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER A 66 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET A 95 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER A 66 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET A 95 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N TYR A 113 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR A 90 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 132 removed outlier: 4.489A pdb=" N GLY A 131 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY B 141 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.573A pdb=" N ILE B 72 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL B 103 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 105 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE B 76 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN B 107 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 131 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLY B 106 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU B 133 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.573A pdb=" N ILE B 72 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL B 103 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 105 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE B 76 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN B 107 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET B 125 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR B 102 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 29 through 32 removed outlier: 5.349A pdb=" N SER C 66 " --> pdb=" O MET C 93 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N MET C 95 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 32 removed outlier: 5.349A pdb=" N SER C 66 " --> pdb=" O MET C 93 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N MET C 95 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR C 113 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR C 90 " --> pdb=" O TYR C 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 126 through 132 removed outlier: 4.443A pdb=" N GLY C 131 " --> pdb=" O GLY D 141 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY D 141 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.574A pdb=" N ILE D 72 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL D 103 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU D 105 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE D 76 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN D 107 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG D 131 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY D 106 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU D 133 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA D 108 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.574A pdb=" N ILE D 72 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL D 103 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU D 105 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE D 76 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN D 107 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET D 125 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR D 102 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER E 66 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET E 95 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER E 66 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET E 95 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR E 113 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR E 90 " --> pdb=" O TYR E 113 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 126 through 132 removed outlier: 4.564A pdb=" N GLY E 131 " --> pdb=" O GLY F 141 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY F 141 " --> pdb=" O GLY E 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 41 through 44 removed outlier: 6.574A pdb=" N ILE F 72 " --> pdb=" O GLN F 101 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL F 103 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET F 74 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU F 105 " --> pdb=" O MET F 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE F 76 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN F 107 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG F 131 " --> pdb=" O CYS F 104 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY F 106 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU F 133 " --> pdb=" O GLY F 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA F 108 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 41 through 44 removed outlier: 6.574A pdb=" N ILE F 72 " --> pdb=" O GLN F 101 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL F 103 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET F 74 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU F 105 " --> pdb=" O MET F 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE F 76 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN F 107 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET F 125 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR F 102 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER G 66 " --> pdb=" O MET G 93 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N MET G 95 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER G 66 " --> pdb=" O MET G 93 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N MET G 95 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR G 113 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR G 90 " --> pdb=" O TYR G 113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 126 through 132 removed outlier: 4.599A pdb=" N GLY G 131 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY H 141 " --> pdb=" O GLY G 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.574A pdb=" N ILE H 72 " --> pdb=" O GLN H 101 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL H 103 " --> pdb=" O ILE H 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET H 74 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU H 105 " --> pdb=" O MET H 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE H 76 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN H 107 " --> pdb=" O ILE H 76 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG H 131 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY H 106 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU H 133 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.574A pdb=" N ILE H 72 " --> pdb=" O GLN H 101 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL H 103 " --> pdb=" O ILE H 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET H 74 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU H 105 " --> pdb=" O MET H 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE H 76 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN H 107 " --> pdb=" O ILE H 76 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N MET H 125 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR H 102 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR I 113 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR I 90 " --> pdb=" O TYR I 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 126 through 132 removed outlier: 4.456A pdb=" N GLY I 131 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY J 141 " --> pdb=" O GLY I 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 41 through 44 removed outlier: 6.574A pdb=" N ILE J 72 " --> pdb=" O GLN J 101 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL J 103 " --> pdb=" O ILE J 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET J 74 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU J 105 " --> pdb=" O MET J 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE J 76 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN J 107 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG J 131 " --> pdb=" O CYS J 104 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY J 106 " --> pdb=" O ARG J 131 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU J 133 " --> pdb=" O GLY J 106 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA J 108 " --> pdb=" O LEU J 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 41 through 44 removed outlier: 6.574A pdb=" N ILE J 72 " --> pdb=" O GLN J 101 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL J 103 " --> pdb=" O ILE J 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET J 74 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU J 105 " --> pdb=" O MET J 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE J 76 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN J 107 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N MET J 125 " --> pdb=" O ILE J 100 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR J 102 " --> pdb=" O MET J 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N TYR K 113 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR K 90 " --> pdb=" O TYR K 113 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 126 through 132 removed outlier: 4.536A pdb=" N GLY K 131 " --> pdb=" O GLY L 141 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY L 141 " --> pdb=" O GLY K 131 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 41 through 44 removed outlier: 6.575A pdb=" N ILE L 72 " --> pdb=" O GLN L 101 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL L 103 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET L 74 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU L 105 " --> pdb=" O MET L 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE L 76 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN L 107 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG L 131 " --> pdb=" O CYS L 104 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY L 106 " --> pdb=" O ARG L 131 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU L 133 " --> pdb=" O GLY L 106 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA L 108 " --> pdb=" O LEU L 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 41 through 44 removed outlier: 6.575A pdb=" N ILE L 72 " --> pdb=" O GLN L 101 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL L 103 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET L 74 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU L 105 " --> pdb=" O MET L 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE L 76 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN L 107 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET L 125 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR L 102 " --> pdb=" O MET L 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 29 through 32 removed outlier: 5.350A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR M 113 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR M 90 " --> pdb=" O TYR M 113 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 126 through 132 removed outlier: 4.610A pdb=" N GLY M 131 " --> pdb=" O GLY N 141 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY N 141 " --> pdb=" O GLY M 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 41 through 44 removed outlier: 6.574A pdb=" N ILE N 72 " --> pdb=" O GLN N 101 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL N 103 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET N 74 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU N 105 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE N 76 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN N 107 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG N 131 " --> pdb=" O CYS N 104 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY N 106 " --> pdb=" O ARG N 131 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU N 133 " --> pdb=" O GLY N 106 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA N 108 " --> pdb=" O LEU N 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 41 through 44 removed outlier: 6.574A pdb=" N ILE N 72 " --> pdb=" O GLN N 101 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL N 103 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET N 74 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU N 105 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE N 76 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN N 107 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET N 125 " --> pdb=" O ILE N 100 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR N 102 " --> pdb=" O MET N 125 " (cutoff:3.500A) 1317 hydrogen bonds defined for protein. 3846 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: 7.09 Time building geometry restraints manager: 6.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6494 1.34 - 1.46: 3060 1.46 - 1.58: 10074 1.58 - 1.69: 14 1.69 - 1.81: 217 Bond restraints: 19859 Sorted by residual: bond pdb=" B26 BO2 I 201 " pdb=" O28 BO2 I 201 " ideal model delta sigma weight residual 1.356 1.482 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" B26 BO2 G 201 " pdb=" O28 BO2 G 201 " ideal model delta sigma weight residual 1.356 1.482 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" B26 BO2 C 201 " pdb=" O28 BO2 C 201 " ideal model delta sigma weight residual 1.356 1.482 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" B26 BO2 E 201 " pdb=" O28 BO2 E 201 " ideal model delta sigma weight residual 1.356 1.482 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" B26 BO2 A 201 " pdb=" O28 BO2 A 201 " ideal model delta sigma weight residual 1.356 1.481 -0.125 2.00e-02 2.50e+03 3.92e+01 ... (remaining 19854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 26409 3.11 - 6.22: 349 6.22 - 9.33: 44 9.33 - 12.45: 22 12.45 - 15.56: 14 Bond angle restraints: 26838 Sorted by residual: angle pdb=" O27 BO2 J 301 " pdb=" B26 BO2 J 301 " pdb=" O28 BO2 J 301 " ideal model delta sigma weight residual 119.22 103.66 15.56 3.00e+00 1.11e-01 2.69e+01 angle pdb=" O27 BO2 B 301 " pdb=" B26 BO2 B 301 " pdb=" O28 BO2 B 301 " ideal model delta sigma weight residual 119.22 103.67 15.55 3.00e+00 1.11e-01 2.69e+01 angle pdb=" O27 BO2 D 301 " pdb=" B26 BO2 D 301 " pdb=" O28 BO2 D 301 " ideal model delta sigma weight residual 119.22 103.81 15.41 3.00e+00 1.11e-01 2.64e+01 angle pdb=" O27 BO2 N 301 " pdb=" B26 BO2 N 301 " pdb=" O28 BO2 N 301 " ideal model delta sigma weight residual 119.22 104.09 15.13 3.00e+00 1.11e-01 2.54e+01 angle pdb=" O27 BO2 L 301 " pdb=" B26 BO2 L 301 " pdb=" O28 BO2 L 301 " ideal model delta sigma weight residual 119.22 104.12 15.10 3.00e+00 1.11e-01 2.53e+01 ... (remaining 26833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 11406 14.26 - 28.53: 478 28.53 - 42.79: 180 42.79 - 57.05: 54 57.05 - 71.32: 27 Dihedral angle restraints: 12145 sinusoidal: 4907 harmonic: 7238 Sorted by residual: dihedral pdb=" CA PHE J 43 " pdb=" C PHE J 43 " pdb=" N LEU J 44 " pdb=" CA LEU J 44 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PHE H 43 " pdb=" C PHE H 43 " pdb=" N LEU H 44 " pdb=" CA LEU H 44 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PHE F 43 " pdb=" C PHE F 43 " pdb=" N LEU F 44 " pdb=" CA LEU F 44 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 12142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2179 0.049 - 0.098: 685 0.098 - 0.147: 195 0.147 - 0.196: 21 0.196 - 0.245: 7 Chirality restraints: 3087 Sorted by residual: chirality pdb=" CG LEU E 115 " pdb=" CB LEU E 115 " pdb=" CD1 LEU E 115 " pdb=" CD2 LEU E 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU M 115 " pdb=" CB LEU M 115 " pdb=" CD1 LEU M 115 " pdb=" CD2 LEU M 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CG LEU K 115 " pdb=" CB LEU K 115 " pdb=" CD1 LEU K 115 " pdb=" CD2 LEU K 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 3084 not shown) Planarity restraints: 3479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BO2 G 201 " 0.187 2.00e-02 2.50e+03 2.41e-01 7.23e+02 pdb=" C18 BO2 G 201 " -0.077 2.00e-02 2.50e+03 pdb=" C21 BO2 G 201 " 0.289 2.00e-02 2.50e+03 pdb=" N20 BO2 G 201 " -0.406 2.00e-02 2.50e+03 pdb=" O19 BO2 G 201 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 A 201 " 0.187 2.00e-02 2.50e+03 2.38e-01 7.10e+02 pdb=" C18 BO2 A 201 " -0.077 2.00e-02 2.50e+03 pdb=" C21 BO2 A 201 " 0.286 2.00e-02 2.50e+03 pdb=" N20 BO2 A 201 " -0.402 2.00e-02 2.50e+03 pdb=" O19 BO2 A 201 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 I 201 " 0.185 2.00e-02 2.50e+03 2.37e-01 7.02e+02 pdb=" C18 BO2 I 201 " -0.075 2.00e-02 2.50e+03 pdb=" C21 BO2 I 201 " 0.284 2.00e-02 2.50e+03 pdb=" N20 BO2 I 201 " -0.400 2.00e-02 2.50e+03 pdb=" O19 BO2 I 201 " 0.006 2.00e-02 2.50e+03 ... (remaining 3476 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5730 2.80 - 3.33: 19186 3.33 - 3.85: 37941 3.85 - 4.38: 45768 4.38 - 4.90: 74249 Nonbonded interactions: 182874 Sorted by model distance: nonbonded pdb=" OH TYR D 206 " pdb=" OD1 ASP F 91 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR J 206 " pdb=" OD1 ASP L 91 " model vdw 2.300 3.040 nonbonded pdb=" NH2 ARG A 23 " pdb=" OE2 GLU M 54 " model vdw 2.340 3.120 nonbonded pdb=" OH TYR L 206 " pdb=" OD1 ASP N 91 " model vdw 2.343 3.040 nonbonded pdb=" OD1 ASP B 91 " pdb=" OH TYR N 206 " model vdw 2.344 3.040 ... (remaining 182869 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } 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=0.00 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: 1.010 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: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 46.230 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.170 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:10.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.008 0.126 19873 Z= 0.411 Angle : 1.049 15.558 26838 Z= 0.554 Chirality : 0.052 0.245 3087 Planarity : 0.016 0.241 3479 Dihedral : 10.872 71.318 7483 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.35 % Allowed : 3.93 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.13), residues: 2478 helix: -2.71 (0.09), residues: 1393 sheet: -2.18 (0.32), residues: 168 loop : -1.53 (0.18), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP M 174 HIS 0.017 0.003 HIS A 117 PHE 0.026 0.005 PHE J 147 TYR 0.053 0.005 TYR M 63 ARG 0.005 0.001 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.18879 ( 1212) hydrogen bonds : angle 7.70708 ( 3846) covalent geometry : bond 0.00821 (19859) covalent geometry : angle 1.04865 (26838) Misc. bond : bond 0.03399 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 832 time to evaluate : 2.171 Fit side-chains REVERT: A 109 LYS cc_start: 0.7893 (mptm) cc_final: 0.7036 (tmtt) REVERT: E 109 LYS cc_start: 0.7938 (mptm) cc_final: 0.7128 (tmtt) REVERT: E 162 ILE cc_start: 0.8388 (tt) cc_final: 0.8183 (tt) REVERT: F 125 MET cc_start: 0.7963 (mpt) cc_final: 0.7385 (mpt) REVERT: F 151 GLU cc_start: 0.7600 (tt0) cc_final: 0.7334 (mt-10) REVERT: H 93 MET cc_start: 0.8850 (mtp) cc_final: 0.8630 (mtp) REVERT: I 81 MET cc_start: 0.8614 (mtp) cc_final: 0.8321 (mtp) REVERT: I 109 LYS cc_start: 0.7887 (mptm) cc_final: 0.7042 (tmtt) REVERT: J 87 MET cc_start: 0.8611 (mmt) cc_final: 0.8383 (mmm) REVERT: K 109 LYS cc_start: 0.8017 (mptm) cc_final: 0.7129 (tmtt) REVERT: M 109 LYS cc_start: 0.7893 (mptm) cc_final: 0.6989 (mmtt) REVERT: N 55 ASP cc_start: 0.7892 (m-30) cc_final: 0.7674 (m-30) REVERT: N 192 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7197 (mm-30) outliers start: 7 outliers final: 7 residues processed: 832 average time/residue: 1.4789 time to fit residues: 1363.6490 Evaluate side-chains 627 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 620 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain M residue 36 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 222 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN B 146 GLN ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 160 GLN ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN F 101 GLN F 153 GLN G 42 ASN G 124 GLN G 154 ASN G 160 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 GLN J 34 ASN J 101 GLN J 144 GLN ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 GLN ** K 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN L 146 GLN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN M 160 GLN N 153 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.132400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.123501 restraints weight = 17993.062| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 0.72 r_work: 0.3222 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19873 Z= 0.198 Angle : 0.627 7.631 26838 Z= 0.319 Chirality : 0.044 0.187 3087 Planarity : 0.004 0.029 3479 Dihedral : 10.193 59.343 2996 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.09 % Allowed : 12.84 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 2478 helix: 0.01 (0.12), residues: 1393 sheet: -2.53 (0.28), residues: 182 loop : -1.17 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 174 HIS 0.008 0.002 HIS K 117 PHE 0.016 0.003 PHE H 147 TYR 0.017 0.002 TYR G 63 ARG 0.006 0.001 ARG E 152 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 1212) hydrogen bonds : angle 4.66530 ( 3846) covalent geometry : bond 0.00413 (19859) covalent geometry : angle 0.62736 (26838) Misc. bond : bond 0.00045 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 631 time to evaluate : 2.148 Fit side-chains REVERT: A 109 LYS cc_start: 0.8283 (mptm) cc_final: 0.7536 (mmtt) REVERT: C 109 LYS cc_start: 0.8269 (mptm) cc_final: 0.7515 (mmtt) REVERT: E 109 LYS cc_start: 0.8279 (mptm) cc_final: 0.7557 (tmtt) REVERT: F 181 LYS cc_start: 0.8636 (mttm) cc_final: 0.8321 (mtmp) REVERT: I 109 LYS cc_start: 0.8295 (mptm) cc_final: 0.7535 (tmtt) REVERT: J 69 ASP cc_start: 0.7868 (m-30) cc_final: 0.7638 (m-30) REVERT: K 109 LYS cc_start: 0.8334 (mptm) cc_final: 0.7526 (tmtt) REVERT: M 109 LYS cc_start: 0.8281 (mptm) cc_final: 0.7572 (mmtt) REVERT: N 192 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7874 (mm-30) outliers start: 62 outliers final: 30 residues processed: 654 average time/residue: 1.6334 time to fit residues: 1173.9207 Evaluate side-chains 594 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 564 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 224 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 136 GLN B 144 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN D 34 ASN D 59 GLN D 136 GLN E 42 ASN F 136 GLN F 153 GLN G 42 ASN G 154 ASN H 34 ASN H 59 GLN H 129 ASN H 136 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN J 144 GLN ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN L 136 GLN L 144 GLN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN N 153 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.121826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.113207 restraints weight = 17795.617| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 0.68 r_work: 0.3078 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 19873 Z= 0.338 Angle : 0.740 9.636 26838 Z= 0.377 Chirality : 0.050 0.323 3087 Planarity : 0.005 0.044 3479 Dihedral : 10.543 58.262 2996 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.68 % Allowed : 14.19 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2478 helix: 0.76 (0.13), residues: 1414 sheet: -2.64 (0.26), residues: 182 loop : -1.19 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 174 HIS 0.009 0.003 HIS K 117 PHE 0.015 0.003 PHE C 143 TYR 0.022 0.002 TYR G 63 ARG 0.006 0.001 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.05461 ( 1212) hydrogen bonds : angle 4.59674 ( 3846) covalent geometry : bond 0.00721 (19859) covalent geometry : angle 0.73978 (26838) Misc. bond : bond 0.00146 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 539 time to evaluate : 2.150 Fit side-chains REVERT: A 109 LYS cc_start: 0.8578 (mptm) cc_final: 0.7874 (tmtt) REVERT: B 157 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8762 (tp) REVERT: C 43 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7836 (ttp-110) REVERT: C 109 LYS cc_start: 0.8583 (mptm) cc_final: 0.7893 (tmtt) REVERT: E 109 LYS cc_start: 0.8535 (mptm) cc_final: 0.7856 (tmtt) REVERT: E 150 MET cc_start: 0.9037 (mmm) cc_final: 0.8804 (mmm) REVERT: F 49 ASP cc_start: 0.8747 (p0) cc_final: 0.8429 (p0) REVERT: F 161 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7987 (ttt-90) REVERT: F 181 LYS cc_start: 0.8685 (mttm) cc_final: 0.8377 (mtmp) REVERT: G 43 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7848 (ttp-110) REVERT: H 125 MET cc_start: 0.8859 (mpt) cc_final: 0.8579 (mmm) REVERT: H 181 LYS cc_start: 0.8657 (mttm) cc_final: 0.8347 (mtmp) REVERT: I 43 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7892 (ttp-110) REVERT: I 109 LYS cc_start: 0.8586 (mptm) cc_final: 0.7869 (tmtt) REVERT: J 125 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8458 (mmm) REVERT: J 161 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8557 (ttt-90) REVERT: K 43 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7871 (ttp-110) REVERT: K 109 LYS cc_start: 0.8579 (mptm) cc_final: 0.7835 (tmtt) REVERT: M 43 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7861 (ttp-110) REVERT: M 109 LYS cc_start: 0.8516 (mptm) cc_final: 0.7852 (tmtt) REVERT: N 161 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8005 (ttt-90) REVERT: N 192 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7862 (mm-30) outliers start: 74 outliers final: 41 residues processed: 571 average time/residue: 1.6322 time to fit residues: 1023.0923 Evaluate side-chains 564 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 513 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 43 ARG Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 43 ARG Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 43 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 161 ARG Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 117 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 153 GLN E 42 ASN F 153 GLN G 42 ASN H 34 ASN H 54 ASN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN J 59 GLN J 101 GLN J 144 GLN K 42 ASN L 34 ASN L 144 GLN L 153 GLN N 59 GLN N 144 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.132324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.123095 restraints weight = 17986.254| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 0.76 r_work: 0.3213 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19873 Z= 0.164 Angle : 0.587 7.726 26838 Z= 0.294 Chirality : 0.044 0.209 3087 Planarity : 0.003 0.029 3479 Dihedral : 9.950 59.486 2996 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.04 % Allowed : 15.28 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2478 helix: 1.31 (0.13), residues: 1407 sheet: -2.53 (0.27), residues: 182 loop : -1.21 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 174 HIS 0.008 0.002 HIS K 117 PHE 0.008 0.002 PHE C 175 TYR 0.011 0.001 TYR E 91 ARG 0.005 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 1212) hydrogen bonds : angle 4.26288 ( 3846) covalent geometry : bond 0.00343 (19859) covalent geometry : angle 0.58702 (26838) Misc. bond : bond 0.00055 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 586 time to evaluate : 2.116 Fit side-chains REVERT: A 109 LYS cc_start: 0.8364 (mptm) cc_final: 0.7624 (tmtt) REVERT: B 192 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7735 (mm-30) REVERT: C 109 LYS cc_start: 0.8344 (mptm) cc_final: 0.7593 (tmtt) REVERT: E 109 LYS cc_start: 0.8331 (mptm) cc_final: 0.7619 (mmtt) REVERT: E 150 MET cc_start: 0.9024 (mmm) cc_final: 0.8821 (mmm) REVERT: G 43 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7799 (ttp-110) REVERT: H 54 ASN cc_start: 0.8628 (m-40) cc_final: 0.8305 (m-40) REVERT: H 125 MET cc_start: 0.8657 (mpt) cc_final: 0.8443 (mmm) REVERT: I 109 LYS cc_start: 0.8338 (mptm) cc_final: 0.7596 (tmtt) REVERT: J 69 ASP cc_start: 0.7926 (m-30) cc_final: 0.7603 (m-30) REVERT: K 109 LYS cc_start: 0.8338 (mptm) cc_final: 0.7579 (tmtt) REVERT: L 161 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8279 (ttt90) REVERT: M 35 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: M 109 LYS cc_start: 0.8360 (mptm) cc_final: 0.7659 (tmtt) REVERT: N 192 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7730 (mm-30) outliers start: 61 outliers final: 37 residues processed: 604 average time/residue: 1.6822 time to fit residues: 1119.2535 Evaluate side-chains 589 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 549 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 161 ARG Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 118 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 153 GLN E 42 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 ASN H 34 ASN H 136 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN K 42 ASN L 34 ASN L 59 GLN N 136 GLN N 144 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.125149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.115015 restraints weight = 17821.179| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.83 r_work: 0.3097 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 19873 Z= 0.313 Angle : 0.713 9.162 26838 Z= 0.363 Chirality : 0.049 0.303 3087 Planarity : 0.004 0.036 3479 Dihedral : 10.460 59.463 2996 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.48 % Allowed : 15.03 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2478 helix: 1.19 (0.13), residues: 1421 sheet: -2.52 (0.25), residues: 196 loop : -1.19 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 174 HIS 0.008 0.002 HIS K 117 PHE 0.013 0.003 PHE E 102 TYR 0.014 0.002 TYR G 63 ARG 0.006 0.001 ARG M 152 Details of bonding type rmsd hydrogen bonds : bond 0.05291 ( 1212) hydrogen bonds : angle 4.41805 ( 3846) covalent geometry : bond 0.00664 (19859) covalent geometry : angle 0.71326 (26838) Misc. bond : bond 0.00130 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 526 time to evaluate : 2.390 Fit side-chains REVERT: A 109 LYS cc_start: 0.8562 (mptm) cc_final: 0.7783 (tmtt) REVERT: C 43 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7758 (ttp-110) REVERT: C 109 LYS cc_start: 0.8591 (mptm) cc_final: 0.7815 (tmtt) REVERT: E 109 LYS cc_start: 0.8505 (mptm) cc_final: 0.7731 (tmtt) REVERT: E 150 MET cc_start: 0.9052 (mmm) cc_final: 0.8810 (mmp) REVERT: F 35 LYS cc_start: 0.8602 (tptm) cc_final: 0.8396 (tmtt) REVERT: F 49 ASP cc_start: 0.8739 (p0) cc_final: 0.8389 (p0) REVERT: F 161 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7860 (ttt-90) REVERT: G 17 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8247 (t) REVERT: G 43 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7735 (ttp-110) REVERT: H 125 MET cc_start: 0.8878 (mpt) cc_final: 0.8645 (mmm) REVERT: H 157 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8544 (tp) REVERT: I 109 LYS cc_start: 0.8577 (mptm) cc_final: 0.7769 (tmtt) REVERT: J 161 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8369 (ttt-90) REVERT: K 43 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7816 (ttp-110) REVERT: K 109 LYS cc_start: 0.8593 (mptm) cc_final: 0.7782 (tmtt) REVERT: L 125 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8580 (mtp) REVERT: M 35 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: M 43 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7780 (ttp-110) REVERT: M 109 LYS cc_start: 0.8538 (mptm) cc_final: 0.7776 (tmtt) REVERT: N 125 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8344 (mtp) REVERT: N 161 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7963 (ttt-90) REVERT: N 192 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7889 (tp30) outliers start: 70 outliers final: 44 residues processed: 547 average time/residue: 1.6873 time to fit residues: 1011.3045 Evaluate side-chains 566 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 510 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 43 ARG Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ARG Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 125 MET Chi-restraints excluded: chain N residue 161 ARG Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 186 optimal weight: 2.9990 chunk 211 optimal weight: 0.0060 chunk 89 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN E 42 ASN F 59 GLN G 42 ASN H 34 ASN H 153 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN K 42 ASN L 34 ASN L 153 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.131387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.122255 restraints weight = 18028.805| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 0.75 r_work: 0.3208 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19873 Z= 0.164 Angle : 0.591 7.608 26838 Z= 0.296 Chirality : 0.044 0.213 3087 Planarity : 0.003 0.031 3479 Dihedral : 9.953 59.227 2996 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.29 % Allowed : 15.73 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.16), residues: 2478 helix: 1.50 (0.13), residues: 1407 sheet: -2.52 (0.27), residues: 182 loop : -1.23 (0.18), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 174 HIS 0.007 0.002 HIS C 117 PHE 0.008 0.002 PHE E 102 TYR 0.007 0.001 TYR K 91 ARG 0.007 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 1212) hydrogen bonds : angle 4.19766 ( 3846) covalent geometry : bond 0.00346 (19859) covalent geometry : angle 0.59082 (26838) Misc. bond : bond 0.00053 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 577 time to evaluate : 2.223 Fit side-chains REVERT: A 109 LYS cc_start: 0.8398 (mptm) cc_final: 0.7649 (tmtt) REVERT: B 192 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7719 (mm-30) REVERT: C 109 LYS cc_start: 0.8387 (mptm) cc_final: 0.7643 (tmtt) REVERT: E 39 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7422 (tm-30) REVERT: E 109 LYS cc_start: 0.8363 (mptm) cc_final: 0.7656 (tmtt) REVERT: F 35 LYS cc_start: 0.8584 (tptm) cc_final: 0.8369 (tmtt) REVERT: G 17 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8267 (t) REVERT: H 54 ASN cc_start: 0.8659 (m-40) cc_final: 0.8332 (m-40) REVERT: I 109 LYS cc_start: 0.8361 (mptm) cc_final: 0.7607 (tmtt) REVERT: J 125 MET cc_start: 0.8905 (mpp) cc_final: 0.8542 (mpp) REVERT: J 161 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8254 (ttt-90) REVERT: K 109 LYS cc_start: 0.8371 (mptm) cc_final: 0.7612 (tmtt) REVERT: L 69 ASP cc_start: 0.7991 (m-30) cc_final: 0.7653 (m-30) REVERT: M 35 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: M 38 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7309 (t0) REVERT: M 43 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7803 (ttp-110) REVERT: M 109 LYS cc_start: 0.8394 (mptm) cc_final: 0.7698 (tmtt) REVERT: N 192 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7887 (mm-30) outliers start: 66 outliers final: 35 residues processed: 599 average time/residue: 1.6593 time to fit residues: 1091.8665 Evaluate side-chains 594 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 554 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ARG Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 189 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 219 optimal weight: 0.5980 chunk 183 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN E 42 ASN F 34 ASN G 42 ASN H 34 ASN H 136 GLN H 153 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN K 42 ASN L 34 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.132417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122455 restraints weight = 17854.499| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.84 r_work: 0.3207 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19873 Z= 0.162 Angle : 0.587 7.612 26838 Z= 0.295 Chirality : 0.044 0.214 3087 Planarity : 0.003 0.029 3479 Dihedral : 9.961 59.410 2996 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.99 % Allowed : 16.92 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2478 helix: 1.57 (0.13), residues: 1414 sheet: -2.44 (0.28), residues: 182 loop : -1.19 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 174 HIS 0.006 0.002 HIS K 117 PHE 0.009 0.002 PHE I 102 TYR 0.009 0.001 TYR M 91 ARG 0.007 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 1212) hydrogen bonds : angle 4.13310 ( 3846) covalent geometry : bond 0.00342 (19859) covalent geometry : angle 0.58728 (26838) Misc. bond : bond 0.00052 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 555 time to evaluate : 2.391 Fit side-chains REVERT: A 109 LYS cc_start: 0.8393 (mptm) cc_final: 0.7590 (tmtt) REVERT: B 47 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7074 (tp40) REVERT: B 192 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7689 (mm-30) REVERT: C 109 LYS cc_start: 0.8360 (mptm) cc_final: 0.7584 (tmtt) REVERT: D 125 MET cc_start: 0.8657 (mpt) cc_final: 0.8442 (mmm) REVERT: E 39 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7275 (pm20) REVERT: E 109 LYS cc_start: 0.8362 (mptm) cc_final: 0.7605 (tmtt) REVERT: F 35 LYS cc_start: 0.8544 (tptm) cc_final: 0.8317 (tmtt) REVERT: F 47 GLN cc_start: 0.7338 (tp40) cc_final: 0.6994 (tp40) REVERT: H 54 ASN cc_start: 0.8618 (m-40) cc_final: 0.8266 (m-40) REVERT: I 109 LYS cc_start: 0.8333 (mptm) cc_final: 0.7551 (tmtt) REVERT: J 47 GLN cc_start: 0.7155 (tp40) cc_final: 0.6889 (tp40) REVERT: J 69 ASP cc_start: 0.7956 (m-30) cc_final: 0.7589 (m-30) REVERT: J 161 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8229 (ttt-90) REVERT: J 202 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8398 (t) REVERT: K 43 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7945 (ttp-110) REVERT: K 109 LYS cc_start: 0.8348 (mptm) cc_final: 0.7547 (tmtt) REVERT: L 69 ASP cc_start: 0.8011 (m-30) cc_final: 0.7652 (m-30) REVERT: M 35 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: M 38 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7319 (t0) REVERT: M 43 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7757 (ttp-110) REVERT: M 109 LYS cc_start: 0.8391 (mptm) cc_final: 0.7623 (tmtt) REVERT: N 192 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7754 (mm-30) outliers start: 60 outliers final: 37 residues processed: 569 average time/residue: 1.6990 time to fit residues: 1063.0510 Evaluate side-chains 578 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 534 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 43 ARG Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ARG Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 189 optimal weight: 0.0980 chunk 179 optimal weight: 10.0000 chunk 125 optimal weight: 0.2980 chunk 74 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 153 GLN E 42 ASN G 42 ASN H 34 ASN H 101 GLN H 153 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN K 42 ASN L 34 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.127464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.117433 restraints weight = 17944.623| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 0.84 r_work: 0.3126 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19873 Z= 0.242 Angle : 0.659 8.764 26838 Z= 0.334 Chirality : 0.046 0.264 3087 Planarity : 0.004 0.035 3479 Dihedral : 10.195 59.935 2996 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.04 % Allowed : 17.57 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.30 (0.16), residues: 2478 helix: 1.40 (0.13), residues: 1421 sheet: -2.45 (0.28), residues: 182 loop : -1.17 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 174 HIS 0.007 0.002 HIS K 117 PHE 0.012 0.002 PHE I 102 TYR 0.011 0.002 TYR L 95 ARG 0.005 0.001 ARG I 152 Details of bonding type rmsd hydrogen bonds : bond 0.04741 ( 1212) hydrogen bonds : angle 4.27315 ( 3846) covalent geometry : bond 0.00511 (19859) covalent geometry : angle 0.65863 (26838) Misc. bond : bond 0.00097 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 526 time to evaluate : 2.068 Fit side-chains REVERT: A 109 LYS cc_start: 0.8527 (mptm) cc_final: 0.7740 (tmtt) REVERT: C 43 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7770 (ttp-110) REVERT: C 109 LYS cc_start: 0.8502 (mptm) cc_final: 0.7716 (tmtt) REVERT: E 109 LYS cc_start: 0.8449 (mptm) cc_final: 0.7703 (tmtt) REVERT: I 109 LYS cc_start: 0.8483 (mptm) cc_final: 0.7673 (tmtt) REVERT: J 161 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8343 (ttt-90) REVERT: K 43 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7815 (ttp-110) REVERT: K 109 LYS cc_start: 0.8507 (mptm) cc_final: 0.7732 (tmtt) REVERT: M 35 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: M 38 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7368 (t0) REVERT: M 43 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7778 (ttp-110) REVERT: M 109 LYS cc_start: 0.8490 (mptm) cc_final: 0.7735 (tmtt) REVERT: N 192 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7858 (mm-30) outliers start: 61 outliers final: 39 residues processed: 543 average time/residue: 1.7774 time to fit residues: 1056.9724 Evaluate side-chains 564 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 519 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 43 ARG Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 49 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 153 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN E 42 ASN F 34 ASN G 42 ASN H 34 ASN H 101 GLN H 153 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN L 153 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.127731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.117715 restraints weight = 17790.433| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 0.84 r_work: 0.3125 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19873 Z= 0.238 Angle : 0.663 10.298 26838 Z= 0.336 Chirality : 0.046 0.258 3087 Planarity : 0.004 0.034 3479 Dihedral : 10.197 59.870 2996 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.19 % Allowed : 17.72 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2478 helix: 1.37 (0.13), residues: 1421 sheet: -2.45 (0.28), residues: 182 loop : -1.17 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 174 HIS 0.007 0.002 HIS K 117 PHE 0.012 0.002 PHE E 102 TYR 0.011 0.002 TYR L 95 ARG 0.005 0.001 ARG K 152 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 1212) hydrogen bonds : angle 4.27959 ( 3846) covalent geometry : bond 0.00503 (19859) covalent geometry : angle 0.66348 (26838) Misc. bond : bond 0.00091 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 523 time to evaluate : 2.415 Fit side-chains REVERT: A 109 LYS cc_start: 0.8534 (mptm) cc_final: 0.7753 (tmtt) REVERT: B 47 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7249 (tp40) REVERT: C 43 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7758 (ttp-110) REVERT: C 109 LYS cc_start: 0.8502 (mptm) cc_final: 0.7708 (tmtt) REVERT: E 109 LYS cc_start: 0.8444 (mptm) cc_final: 0.7694 (tmtt) REVERT: F 35 LYS cc_start: 0.8571 (tptm) cc_final: 0.8355 (tmtt) REVERT: I 109 LYS cc_start: 0.8493 (mptm) cc_final: 0.7678 (tmtt) REVERT: I 190 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8112 (mm) REVERT: J 161 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8333 (ttt-90) REVERT: K 43 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7808 (ttp-110) REVERT: K 109 LYS cc_start: 0.8509 (mptm) cc_final: 0.7729 (tmtt) REVERT: M 35 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: M 38 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7360 (t0) REVERT: M 43 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7767 (ttp-110) REVERT: M 109 LYS cc_start: 0.8492 (mptm) cc_final: 0.7741 (tmtt) REVERT: N 125 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8803 (mtp) REVERT: N 161 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7911 (ttt-90) REVERT: N 192 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7861 (mm-30) outliers start: 64 outliers final: 42 residues processed: 543 average time/residue: 1.6471 time to fit residues: 980.6492 Evaluate side-chains 574 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 522 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 43 ARG Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 125 MET Chi-restraints excluded: chain N residue 161 ARG Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 176 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 153 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN E 42 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 ASN H 34 ASN H 101 GLN H 153 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN K 42 ASN L 153 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.127192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.117183 restraints weight = 17922.739| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 0.84 r_work: 0.3141 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19873 Z= 0.234 Angle : 0.669 11.854 26838 Z= 0.339 Chirality : 0.046 0.257 3087 Planarity : 0.004 0.034 3479 Dihedral : 10.198 59.702 2996 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.04 % Allowed : 17.92 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2478 helix: 1.36 (0.13), residues: 1421 sheet: -2.43 (0.28), residues: 182 loop : -1.18 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 174 HIS 0.008 0.002 HIS K 117 PHE 0.012 0.002 PHE A 102 TYR 0.012 0.002 TYR B 75 ARG 0.005 0.001 ARG I 152 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 1212) hydrogen bonds : angle 4.28432 ( 3846) covalent geometry : bond 0.00496 (19859) covalent geometry : angle 0.66861 (26838) Misc. bond : bond 0.00088 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 523 time to evaluate : 2.115 Fit side-chains REVERT: A 109 LYS cc_start: 0.8536 (mptm) cc_final: 0.7752 (tmtt) REVERT: C 43 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7764 (ttp-110) REVERT: C 109 LYS cc_start: 0.8504 (mptm) cc_final: 0.7699 (tmtt) REVERT: E 109 LYS cc_start: 0.8444 (mptm) cc_final: 0.7683 (tmtt) REVERT: F 35 LYS cc_start: 0.8578 (tptm) cc_final: 0.8369 (tmtt) REVERT: F 47 GLN cc_start: 0.7589 (tp40) cc_final: 0.7309 (tp40) REVERT: I 109 LYS cc_start: 0.8492 (mptm) cc_final: 0.7671 (tmtt) REVERT: I 190 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8118 (mm) REVERT: J 161 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8316 (ttt-90) REVERT: K 43 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7799 (ttp-110) REVERT: K 109 LYS cc_start: 0.8505 (mptm) cc_final: 0.7715 (tmtt) REVERT: K 164 ARG cc_start: 0.8649 (ttt180) cc_final: 0.8436 (tpt-90) REVERT: M 35 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: M 38 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7382 (t0) REVERT: M 43 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7759 (ttp-110) REVERT: M 109 LYS cc_start: 0.8486 (mptm) cc_final: 0.7726 (tmtt) REVERT: N 47 GLN cc_start: 0.7537 (tp40) cc_final: 0.7099 (tp40) REVERT: N 161 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7918 (ttt-90) REVERT: N 192 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7864 (mm-30) outliers start: 61 outliers final: 44 residues processed: 541 average time/residue: 1.6760 time to fit residues: 993.3077 Evaluate side-chains 569 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 517 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 161 ARG Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 43 ARG Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 161 ARG Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 228 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 153 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN E 42 ASN G 42 ASN H 34 ASN H 101 GLN H 153 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN K 42 ASN L 153 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.133489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.124494 restraints weight = 18140.804| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 0.75 r_work: 0.3242 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19873 Z= 0.149 Angle : 0.597 9.082 26838 Z= 0.299 Chirality : 0.044 0.202 3087 Planarity : 0.003 0.029 3479 Dihedral : 9.927 59.601 2996 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.69 % Allowed : 18.37 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2478 helix: 1.54 (0.13), residues: 1421 sheet: -2.18 (0.31), residues: 196 loop : -1.10 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 174 HIS 0.008 0.002 HIS K 117 PHE 0.011 0.001 PHE A 102 TYR 0.012 0.001 TYR L 95 ARG 0.006 0.000 ARG K 152 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 1212) hydrogen bonds : angle 4.13908 ( 3846) covalent geometry : bond 0.00314 (19859) covalent geometry : angle 0.59692 (26838) Misc. bond : bond 0.00044 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18194.49 seconds wall clock time: 312 minutes 56.12 seconds (18776.12 seconds total)