Starting phenix.real_space_refine on Thu Sep 18 18:11:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yd2_39163/09_2025/8yd2_39163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yd2_39163/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yd2_39163/09_2025/8yd2_39163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yd2_39163/09_2025/8yd2_39163.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yd2_39163/09_2025/8yd2_39163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yd2_39163/09_2025/8yd2_39163.map" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.96, per 1000 atoms: 0.25 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: 1.88 Conformation dependent library (CDL) restraints added in 884.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.91 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: 4.69 Time building geometry restraints manager: 2.41 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: 0.07 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: 1.130 Set stop_for_unknowns flag: 0.010 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.100 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.550 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG A 119 TYR 0.053 0.005 TYR M 63 PHE 0.026 0.005 PHE J 147 TRP 0.008 0.003 TRP M 174 HIS 0.017 0.003 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00821 (19859) covalent geometry : angle 1.04865 (26838) hydrogen bonds : bond 0.18879 ( 1212) hydrogen bonds : angle 7.70708 ( 3846) 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 : 0.805 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: 0.7129 (tmtt) REVERT: F 125 MET cc_start: 0.7963 (mpt) cc_final: 0.7386 (mpt) REVERT: F 151 GLU cc_start: 0.7600 (tt0) cc_final: 0.7357 (mt-10) REVERT: H 93 MET cc_start: 0.8850 (mtp) cc_final: 0.8631 (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: 0.8382 (mmm) REVERT: K 109 LYS cc_start: 0.8017 (mptm) cc_final: 0.7130 (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: 0.7675 (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: 0.7842 time to fit residues: 720.9562 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 : 0.784 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.0470 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 overall best weight: 2.0060 ------------------------------------------------------------------------------- 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 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 59 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 = 0.3399 r_free = 0.3399 target = 0.131282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.122354 restraints weight = 17905.863| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.72 r_work: 0.3206 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19873 Z= 0.214 Angle : 0.635 7.454 26838 Z= 0.324 Chirality : 0.045 0.205 3087 Planarity : 0.004 0.030 3479 Dihedral : 10.248 59.291 2996 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.14 % Allowed : 12.84 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.15), residues: 2478 helix: 0.02 (0.12), residues: 1393 sheet: -2.58 (0.28), residues: 182 loop : -1.17 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 152 TYR 0.018 0.002 TYR G 63 PHE 0.016 0.003 PHE F 147 TRP 0.002 0.001 TRP I 174 HIS 0.009 0.002 HIS K 117 Details of bonding type rmsd covalent geometry : bond 0.00449 (19859) covalent geometry : angle 0.63518 (26838) hydrogen bonds : bond 0.04542 ( 1212) hydrogen bonds : angle 4.67342 ( 3846) Misc. bond : bond 0.00056 ( 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 679 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 616 time to evaluate : 0.923 Fit side-chains REVERT: A 109 LYS cc_start: 0.8377 (mptm) cc_final: 0.7636 (mmtt) REVERT: C 109 LYS cc_start: 0.8359 (mptm) cc_final: 0.7580 (tmtt) REVERT: E 109 LYS cc_start: 0.8324 (mptm) cc_final: 0.7600 (tmtt) REVERT: F 181 LYS cc_start: 0.8643 (mttm) cc_final: 0.8313 (mtmp) REVERT: G 164 ARG cc_start: 0.8621 (tpt170) cc_final: 0.8415 (tpt-90) REVERT: I 109 LYS cc_start: 0.8317 (mptm) cc_final: 0.7568 (tmtt) REVERT: I 164 ARG cc_start: 0.8654 (tpt-90) cc_final: 0.8452 (tpt-90) REVERT: J 69 ASP cc_start: 0.7891 (m-30) cc_final: 0.7657 (m-30) REVERT: K 109 LYS cc_start: 0.8389 (mptm) cc_final: 0.7579 (tmtt) REVERT: M 109 LYS cc_start: 0.8364 (mptm) cc_final: 0.7640 (mmtt) REVERT: N 161 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7928 (ttt-90) REVERT: N 192 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7854 (mm-30) outliers start: 63 outliers final: 30 residues processed: 641 average time/residue: 0.8408 time to fit residues: 591.9657 Evaluate side-chains 589 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 558 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 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 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 36 VAL Chi-restraints excluded: chain M residue 38 ASP 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 161 ARG 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 20 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 160 optimal weight: 0.0170 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 overall best weight: 2.1224 ------------------------------------------------------------------------------- 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 136 GLN B 144 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 59 GLN D 136 GLN E 42 ASN F 136 GLN F 153 GLN G 42 ASN H 34 ASN 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 J 136 GLN J 144 GLN K 42 ASN L 34 ASN 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.129321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.119229 restraints weight = 18022.546| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 0.85 r_work: 0.3152 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19873 Z= 0.214 Angle : 0.628 8.134 26838 Z= 0.317 Chirality : 0.045 0.238 3087 Planarity : 0.004 0.030 3479 Dihedral : 10.198 59.887 2996 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.53 % Allowed : 14.48 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.16), residues: 2478 helix: 0.96 (0.13), residues: 1400 sheet: -2.71 (0.27), residues: 182 loop : -1.07 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 152 TYR 0.014 0.002 TYR G 63 PHE 0.009 0.002 PHE L 147 TRP 0.002 0.001 TRP I 174 HIS 0.008 0.002 HIS K 117 Details of bonding type rmsd covalent geometry : bond 0.00452 (19859) covalent geometry : angle 0.62835 (26838) hydrogen bonds : bond 0.04553 ( 1212) hydrogen bonds : angle 4.46018 ( 3846) Misc. bond : bond 0.00080 ( 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 637 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 566 time to evaluate : 0.797 Fit side-chains REVERT: A 109 LYS cc_start: 0.8425 (mptm) cc_final: 0.7657 (tmtt) REVERT: C 43 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7757 (ttp-110) REVERT: C 109 LYS cc_start: 0.8437 (mptm) cc_final: 0.7634 (tmtt) REVERT: D 125 MET cc_start: 0.8738 (mpt) cc_final: 0.8504 (mmm) REVERT: E 109 LYS cc_start: 0.8401 (mptm) cc_final: 0.7640 (tmtt) REVERT: G 43 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7798 (ttp-110) REVERT: G 164 ARG cc_start: 0.8606 (tpt170) cc_final: 0.8380 (tpt-90) REVERT: H 125 MET cc_start: 0.8745 (mpt) cc_final: 0.8519 (mmm) REVERT: H 192 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7643 (tp30) REVERT: I 109 LYS cc_start: 0.8414 (mptm) cc_final: 0.7613 (tmtt) REVERT: J 69 ASP cc_start: 0.7959 (m-30) cc_final: 0.7683 (m-30) REVERT: J 161 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8498 (ttt-90) REVERT: K 43 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7844 (ttp-110) REVERT: K 109 LYS cc_start: 0.8436 (mptm) cc_final: 0.7607 (tmtt) REVERT: L 125 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8486 (mpp) REVERT: M 35 GLU cc_start: 0.7938 (tt0) cc_final: 0.7734 (tm-30) REVERT: M 43 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7771 (ttp-110) REVERT: M 109 LYS cc_start: 0.8461 (mptm) cc_final: 0.7705 (tmtt) REVERT: N 161 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7902 (ttt-90) REVERT: N 192 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7810 (mm-30) outliers start: 71 outliers final: 40 residues processed: 592 average time/residue: 0.8255 time to fit residues: 535.8530 Evaluate side-chains 604 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 557 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 38 ASP 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 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 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 L residue 125 MET 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 78 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 149 optimal weight: 0.2980 chunk 163 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 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 J 144 GLN K 42 ASN L 34 ASN L 59 GLN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN N 153 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.133564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.124286 restraints weight = 17918.691| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 0.76 r_work: 0.3227 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3012 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= 0.156 Angle : 0.572 7.614 26838 Z= 0.287 Chirality : 0.043 0.199 3087 Planarity : 0.003 0.029 3479 Dihedral : 10.002 59.988 2996 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.89 % Allowed : 14.83 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.16), residues: 2478 helix: 1.44 (0.13), residues: 1393 sheet: -2.58 (0.27), residues: 182 loop : -1.08 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 152 TYR 0.008 0.001 TYR E 91 PHE 0.008 0.002 PHE C 175 TRP 0.002 0.001 TRP G 174 HIS 0.007 0.002 HIS K 117 Details of bonding type rmsd covalent geometry : bond 0.00325 (19859) covalent geometry : angle 0.57249 (26838) hydrogen bonds : bond 0.03970 ( 1212) hydrogen bonds : angle 4.24502 ( 3846) Misc. bond : bond 0.00054 ( 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 658 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 600 time to evaluate : 0.804 Fit side-chains REVERT: A 109 LYS cc_start: 0.8333 (mptm) cc_final: 0.7587 (tmtt) REVERT: B 47 GLN cc_start: 0.7328 (tp40) cc_final: 0.7048 (tp40) REVERT: B 192 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7729 (mm-30) REVERT: C 109 LYS cc_start: 0.8308 (mptm) cc_final: 0.7564 (tmtt) REVERT: D 125 MET cc_start: 0.8590 (mpt) cc_final: 0.8378 (mmm) REVERT: E 109 LYS cc_start: 0.8319 (mptm) cc_final: 0.7600 (tmtt) REVERT: F 181 LYS cc_start: 0.8617 (mttp) cc_final: 0.8241 (mtmp) REVERT: G 17 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8246 (t) REVERT: G 164 ARG cc_start: 0.8609 (tpt170) cc_final: 0.8398 (tpt-90) REVERT: H 125 MET cc_start: 0.8609 (mpt) cc_final: 0.8353 (mmm) REVERT: H 192 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7819 (mm-30) REVERT: I 109 LYS cc_start: 0.8325 (mptm) cc_final: 0.7586 (tmtt) REVERT: K 109 LYS cc_start: 0.8319 (mptm) cc_final: 0.7559 (tmtt) REVERT: M 43 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7821 (ttp-110) REVERT: M 109 LYS cc_start: 0.8335 (mptm) cc_final: 0.7614 (tmtt) REVERT: N 192 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7737 (mm-30) outliers start: 58 outliers final: 36 residues processed: 619 average time/residue: 0.7761 time to fit residues: 526.7631 Evaluate side-chains 585 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 547 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 36 VAL 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 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 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 85 SER 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 137 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 F 59 GLN 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 J 59 GLN J 136 GLN K 42 ASN L 34 ASN L 136 GLN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN N 153 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.127261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.118902 restraints weight = 18160.291| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 0.68 r_work: 0.3154 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19873 Z= 0.197 Angle : 0.606 7.799 26838 Z= 0.306 Chirality : 0.044 0.228 3087 Planarity : 0.004 0.031 3479 Dihedral : 10.057 59.573 2996 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.68 % Allowed : 14.98 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.16), residues: 2478 helix: 1.40 (0.13), residues: 1421 sheet: -2.53 (0.27), residues: 182 loop : -1.16 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 152 TYR 0.010 0.001 TYR K 63 PHE 0.008 0.002 PHE E 102 TRP 0.002 0.001 TRP G 174 HIS 0.007 0.002 HIS K 117 Details of bonding type rmsd covalent geometry : bond 0.00416 (19859) covalent geometry : angle 0.60644 (26838) hydrogen bonds : bond 0.04350 ( 1212) hydrogen bonds : angle 4.24449 ( 3846) Misc. bond : bond 0.00076 ( 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 632 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 558 time to evaluate : 0.767 Fit side-chains REVERT: A 109 LYS cc_start: 0.8456 (mptm) cc_final: 0.7719 (tmtt) REVERT: C 43 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7866 (ttp-110) REVERT: C 109 LYS cc_start: 0.8437 (mptm) cc_final: 0.7727 (tmtt) REVERT: D 125 MET cc_start: 0.8646 (mpt) cc_final: 0.8419 (mmm) REVERT: E 109 LYS cc_start: 0.8430 (mptm) cc_final: 0.7741 (tmtt) REVERT: G 43 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7956 (ttp-110) REVERT: G 120 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8980 (mp) REVERT: G 164 ARG cc_start: 0.8639 (tpt170) cc_final: 0.8439 (tpt-90) REVERT: H 181 LYS cc_start: 0.8659 (mttm) cc_final: 0.8362 (mtmp) REVERT: H 192 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7676 (tp30) REVERT: I 109 LYS cc_start: 0.8439 (mptm) cc_final: 0.7710 (tmtt) REVERT: J 161 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8296 (ttt-90) REVERT: K 43 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7857 (ttp-110) REVERT: K 109 LYS cc_start: 0.8417 (mptm) cc_final: 0.7678 (tmtt) REVERT: M 35 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: M 43 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7840 (ttp-110) REVERT: M 109 LYS cc_start: 0.8421 (mptm) cc_final: 0.7743 (tmtt) REVERT: N 161 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7977 (ttt-90) REVERT: N 192 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7799 (mm-30) outliers start: 74 outliers final: 43 residues processed: 581 average time/residue: 0.7966 time to fit residues: 507.2504 Evaluate side-chains 592 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 541 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 G residue 43 ARG Chi-restraints excluded: chain G residue 120 ILE 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 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 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 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 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 108 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.0070 chunk 177 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 G 42 ASN H 34 ASN H 59 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.137126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.127337 restraints weight = 18046.704| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 0.84 r_work: 0.3268 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19873 Z= 0.127 Angle : 0.547 7.426 26838 Z= 0.273 Chirality : 0.042 0.187 3087 Planarity : 0.003 0.029 3479 Dihedral : 9.758 59.818 2996 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.04 % Allowed : 16.23 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.16), residues: 2478 helix: 1.68 (0.13), residues: 1414 sheet: -2.39 (0.29), residues: 182 loop : -1.13 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 152 TYR 0.010 0.001 TYR L 95 PHE 0.007 0.001 PHE C 175 TRP 0.002 0.000 TRP K 174 HIS 0.006 0.002 HIS K 117 Details of bonding type rmsd covalent geometry : bond 0.00264 (19859) covalent geometry : angle 0.54653 (26838) hydrogen bonds : bond 0.03588 ( 1212) hydrogen bonds : angle 4.05231 ( 3846) Misc. bond : bond 0.00030 ( 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 660 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 599 time to evaluate : 0.576 Fit side-chains REVERT: A 109 LYS cc_start: 0.8210 (mptm) cc_final: 0.7403 (tmtt) REVERT: B 47 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6745 (tp40) REVERT: B 192 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7659 (mm-30) REVERT: C 109 LYS cc_start: 0.8189 (mptm) cc_final: 0.7407 (tmtt) REVERT: E 109 LYS cc_start: 0.8211 (mptm) cc_final: 0.7465 (mmtt) REVERT: F 35 LYS cc_start: 0.8550 (tptm) cc_final: 0.8329 (tmtt) REVERT: F 47 GLN cc_start: 0.6751 (tp40) cc_final: 0.6503 (tp40) REVERT: F 181 LYS cc_start: 0.8595 (mttp) cc_final: 0.8178 (mtmp) REVERT: G 120 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8808 (mp) REVERT: G 152 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8360 (ttp80) REVERT: G 164 ARG cc_start: 0.8569 (tpt170) cc_final: 0.8356 (tpt-90) REVERT: H 181 LYS cc_start: 0.8600 (mttm) cc_final: 0.8228 (mtmp) REVERT: H 192 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7451 (mm-30) REVERT: I 109 LYS cc_start: 0.8208 (mptm) cc_final: 0.7416 (tmtt) REVERT: J 47 GLN cc_start: 0.6878 (tp40) cc_final: 0.6538 (tp40) REVERT: K 109 LYS cc_start: 0.8181 (mptm) cc_final: 0.7400 (tmtt) REVERT: M 38 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7305 (t0) REVERT: M 43 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7758 (ttp-110) REVERT: M 109 LYS cc_start: 0.8212 (mptm) cc_final: 0.7440 (tmtt) REVERT: N 47 GLN cc_start: 0.7047 (tp40) cc_final: 0.6579 (tp40) REVERT: N 125 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8437 (mtp) REVERT: N 192 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7661 (mm-30) outliers start: 61 outliers final: 31 residues processed: 618 average time/residue: 0.7621 time to fit residues: 517.4682 Evaluate side-chains 586 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 550 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 47 GLN 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 17 THR Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 52 SER 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 19 SER Chi-restraints excluded: chain K residue 36 VAL 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 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 125 MET 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 30 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 101 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 N 153 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.130388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.120459 restraints weight = 17968.078| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 0.84 r_work: 0.3180 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19873 Z= 0.193 Angle : 0.611 7.714 26838 Z= 0.309 Chirality : 0.044 0.233 3087 Planarity : 0.004 0.032 3479 Dihedral : 10.005 59.731 2996 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.29 % Allowed : 17.02 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.16), residues: 2478 helix: 1.54 (0.13), residues: 1421 sheet: -2.40 (0.28), residues: 182 loop : -1.11 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 152 TYR 0.010 0.001 TYR L 95 PHE 0.009 0.002 PHE E 102 TRP 0.008 0.001 TRP K 174 HIS 0.006 0.002 HIS K 117 Details of bonding type rmsd covalent geometry : bond 0.00405 (19859) covalent geometry : angle 0.61138 (26838) hydrogen bonds : bond 0.04317 ( 1212) hydrogen bonds : angle 4.19529 ( 3846) Misc. bond : bond 0.00070 ( 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 617 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 551 time to evaluate : 0.573 Fit side-chains REVERT: A 109 LYS cc_start: 0.8436 (mptm) cc_final: 0.7649 (tmtt) REVERT: A 152 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8431 (ttp80) REVERT: B 47 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7170 (tp40) REVERT: C 43 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7768 (ttp-110) REVERT: C 109 LYS cc_start: 0.8403 (mptm) cc_final: 0.7628 (tmtt) REVERT: E 109 LYS cc_start: 0.8415 (mptm) cc_final: 0.7669 (tmtt) REVERT: F 35 LYS cc_start: 0.8560 (tptm) cc_final: 0.8339 (tmtt) REVERT: F 47 GLN cc_start: 0.7445 (tp40) cc_final: 0.7089 (tp40) REVERT: F 181 LYS cc_start: 0.8620 (mttp) cc_final: 0.8228 (mtmp) REVERT: G 120 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8980 (mp) REVERT: G 164 ARG cc_start: 0.8621 (tpt170) cc_final: 0.8419 (tpt-90) REVERT: H 192 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7588 (tp30) REVERT: I 109 LYS cc_start: 0.8409 (mptm) cc_final: 0.7610 (tmtt) REVERT: J 47 GLN cc_start: 0.7364 (tp40) cc_final: 0.7162 (tp40) REVERT: J 143 ILE cc_start: 0.8576 (mt) cc_final: 0.8288 (mt) REVERT: K 109 LYS cc_start: 0.8420 (mptm) cc_final: 0.7634 (tmtt) REVERT: M 38 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7255 (t0) REVERT: M 43 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7778 (ttp-110) REVERT: M 109 LYS cc_start: 0.8447 (mptm) cc_final: 0.7676 (tmtt) REVERT: N 192 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7791 (mm-30) outliers start: 66 outliers final: 43 residues processed: 571 average time/residue: 0.8102 time to fit residues: 506.7633 Evaluate side-chains 572 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 524 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 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 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 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 39 GLU 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 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 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 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 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 40 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 241 optimal weight: 0.0030 chunk 155 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.7196 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 ASN H 34 ASN H 101 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 N 153 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.121151 restraints weight = 18075.073| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 0.75 r_work: 0.3196 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19873 Z= 0.187 Angle : 0.608 8.975 26838 Z= 0.307 Chirality : 0.044 0.224 3087 Planarity : 0.003 0.029 3479 Dihedral : 10.010 59.937 2996 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.99 % Allowed : 17.47 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.16), residues: 2478 helix: 1.54 (0.13), residues: 1421 sheet: -2.40 (0.28), residues: 182 loop : -1.09 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 152 TYR 0.011 0.001 TYR L 95 PHE 0.011 0.002 PHE M 102 TRP 0.006 0.001 TRP K 174 HIS 0.006 0.002 HIS K 117 Details of bonding type rmsd covalent geometry : bond 0.00392 (19859) covalent geometry : angle 0.60831 (26838) hydrogen bonds : bond 0.04235 ( 1212) hydrogen bonds : angle 4.17711 ( 3846) Misc. bond : bond 0.00066 ( 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 596 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 536 time to evaluate : 0.709 Fit side-chains REVERT: A 109 LYS cc_start: 0.8422 (mptm) cc_final: 0.7672 (tmtt) REVERT: B 35 LYS cc_start: 0.8604 (tptp) cc_final: 0.8354 (tmtt) REVERT: B 47 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7184 (tp40) REVERT: B 192 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7822 (mm-30) REVERT: B 202 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8390 (t) REVERT: C 43 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7791 (ttp-110) REVERT: C 109 LYS cc_start: 0.8400 (mptm) cc_final: 0.7680 (tmtt) REVERT: E 38 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7430 (t0) REVERT: E 109 LYS cc_start: 0.8403 (mptm) cc_final: 0.7695 (tmtt) REVERT: F 35 LYS cc_start: 0.8559 (tptm) cc_final: 0.8336 (tmtt) REVERT: F 47 GLN cc_start: 0.7477 (tp40) cc_final: 0.7240 (tp40) REVERT: F 181 LYS cc_start: 0.8644 (mttp) cc_final: 0.8284 (mtmp) REVERT: G 120 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.9002 (mp) REVERT: G 164 ARG cc_start: 0.8623 (tpt170) cc_final: 0.8412 (tpt-90) REVERT: H 47 GLN cc_start: 0.7509 (tp40) cc_final: 0.7187 (tp40) REVERT: H 181 LYS cc_start: 0.8638 (mttm) cc_final: 0.8297 (mtmt) REVERT: H 192 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7661 (tp30) REVERT: I 109 LYS cc_start: 0.8409 (mptm) cc_final: 0.7649 (tmtt) REVERT: J 143 ILE cc_start: 0.8641 (mt) cc_final: 0.8378 (mt) REVERT: K 109 LYS cc_start: 0.8419 (mptm) cc_final: 0.7665 (tmtt) REVERT: M 38 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7317 (t0) REVERT: M 43 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7791 (ttp-110) REVERT: M 109 LYS cc_start: 0.8437 (mptm) cc_final: 0.7717 (tmtt) REVERT: N 161 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7956 (ttt-90) REVERT: N 192 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7680 (tp30) outliers start: 60 outliers final: 37 residues processed: 555 average time/residue: 0.8710 time to fit residues: 528.6399 Evaluate side-chains 576 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 531 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 39 GLU 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 125 MET 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 L residue 85 SER 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 40 ILE Chi-restraints excluded: chain M residue 43 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 155 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 213 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 101 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.123848 restraints weight = 18012.873| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.84 r_work: 0.3223 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3302 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= 0.153 Angle : 0.585 9.746 26838 Z= 0.294 Chirality : 0.044 0.208 3087 Planarity : 0.003 0.029 3479 Dihedral : 9.921 59.891 2996 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.74 % Allowed : 17.72 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.16), residues: 2478 helix: 1.62 (0.13), residues: 1421 sheet: -2.40 (0.28), residues: 182 loop : -1.07 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 152 TYR 0.013 0.001 TYR L 95 PHE 0.009 0.001 PHE M 175 TRP 0.003 0.001 TRP K 174 HIS 0.006 0.002 HIS G 117 Details of bonding type rmsd covalent geometry : bond 0.00320 (19859) covalent geometry : angle 0.58498 (26838) hydrogen bonds : bond 0.03888 ( 1212) hydrogen bonds : angle 4.10690 ( 3846) Misc. bond : bond 0.00045 ( 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 609 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 554 time to evaluate : 0.805 Fit side-chains REVERT: A 109 LYS cc_start: 0.8325 (mptm) cc_final: 0.7520 (tmtt) REVERT: B 35 LYS cc_start: 0.8535 (tptp) cc_final: 0.8278 (tmtt) REVERT: B 47 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6952 (tp40) REVERT: B 192 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7687 (mm-30) REVERT: C 109 LYS cc_start: 0.8286 (mptm) cc_final: 0.7531 (tmtt) REVERT: D 47 GLN cc_start: 0.7111 (tp40) cc_final: 0.6773 (tp40) REVERT: E 38 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7384 (t0) REVERT: E 109 LYS cc_start: 0.8328 (mptm) cc_final: 0.7578 (tmtt) REVERT: F 35 LYS cc_start: 0.8494 (tptm) cc_final: 0.8262 (tmtt) REVERT: F 47 GLN cc_start: 0.7263 (tp40) cc_final: 0.6944 (tp40) REVERT: F 125 MET cc_start: 0.8555 (mpp) cc_final: 0.8307 (mpp) REVERT: F 181 LYS cc_start: 0.8600 (mttp) cc_final: 0.8216 (mtmp) REVERT: F 202 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8350 (t) REVERT: G 120 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8903 (mp) REVERT: H 47 GLN cc_start: 0.7323 (tp40) cc_final: 0.7009 (tp40) REVERT: H 181 LYS cc_start: 0.8573 (mttm) cc_final: 0.8217 (mtmt) REVERT: H 192 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7496 (mm-30) REVERT: I 38 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7430 (t0) REVERT: I 109 LYS cc_start: 0.8308 (mptm) cc_final: 0.7525 (tmtt) REVERT: J 47 GLN cc_start: 0.7140 (tp40) cc_final: 0.6869 (tp40) REVERT: J 143 ILE cc_start: 0.8536 (mt) cc_final: 0.8240 (mt) REVERT: K 38 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7356 (t0) REVERT: K 109 LYS cc_start: 0.8326 (mptm) cc_final: 0.7529 (tmtt) REVERT: M 35 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7416 (tp30) REVERT: M 38 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7260 (t0) REVERT: M 43 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7780 (ttp-110) REVERT: M 109 LYS cc_start: 0.8373 (mptm) cc_final: 0.7610 (tmtt) REVERT: N 47 GLN cc_start: 0.7192 (tp40) cc_final: 0.6747 (tp40) REVERT: N 192 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7716 (mm-30) outliers start: 55 outliers final: 35 residues processed: 570 average time/residue: 0.8613 time to fit residues: 537.2349 Evaluate side-chains 584 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 541 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL 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 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 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 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 39 GLU 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 125 MET 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 L residue 85 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 184 optimal weight: 0.0040 chunk 96 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 213 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 ASN H 34 ASN H 101 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 N 153 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.130978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.121029 restraints weight = 18021.512| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 0.84 r_work: 0.3183 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19873 Z= 0.188 Angle : 0.621 12.571 26838 Z= 0.313 Chirality : 0.045 0.228 3087 Planarity : 0.004 0.029 3479 Dihedral : 10.015 59.695 2996 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.34 % Allowed : 18.67 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.16), residues: 2478 helix: 1.54 (0.13), residues: 1421 sheet: -2.36 (0.28), residues: 182 loop : -1.08 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 152 TYR 0.013 0.001 TYR L 95 PHE 0.010 0.002 PHE M 102 TRP 0.005 0.001 TRP K 174 HIS 0.005 0.002 HIS K 117 Details of bonding type rmsd covalent geometry : bond 0.00395 (19859) covalent geometry : angle 0.62110 (26838) hydrogen bonds : bond 0.04242 ( 1212) hydrogen bonds : angle 4.16372 ( 3846) Misc. bond : bond 0.00063 ( 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 587 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 540 time to evaluate : 0.939 Fit side-chains REVERT: A 109 LYS cc_start: 0.8410 (mptm) cc_final: 0.7600 (tmtt) REVERT: B 35 LYS cc_start: 0.8556 (tptp) cc_final: 0.8307 (tmtt) REVERT: B 47 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.7130 (tp40) REVERT: B 192 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7776 (mm-30) REVERT: C 43 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7777 (ttp-110) REVERT: C 109 LYS cc_start: 0.8395 (mptm) cc_final: 0.7628 (tmtt) REVERT: E 38 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7432 (t0) REVERT: E 109 LYS cc_start: 0.8413 (mptm) cc_final: 0.7659 (tmtt) REVERT: E 163 GLU cc_start: 0.8055 (mp0) cc_final: 0.7718 (mp0) REVERT: F 35 LYS cc_start: 0.8567 (tptm) cc_final: 0.8350 (tmtt) REVERT: F 47 GLN cc_start: 0.7495 (tp40) cc_final: 0.7246 (tp40) REVERT: F 181 LYS cc_start: 0.8609 (mttp) cc_final: 0.8223 (mtmp) REVERT: G 120 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8962 (mp) REVERT: H 47 GLN cc_start: 0.7468 (tp40) cc_final: 0.7148 (tp40) REVERT: H 181 LYS cc_start: 0.8587 (mttm) cc_final: 0.8221 (mtmt) REVERT: H 192 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7559 (tp30) REVERT: I 109 LYS cc_start: 0.8373 (mptm) cc_final: 0.7591 (tmtt) REVERT: J 47 GLN cc_start: 0.7313 (tp40) cc_final: 0.7091 (tp40) REVERT: J 143 ILE cc_start: 0.8628 (mt) cc_final: 0.8368 (mt) REVERT: K 38 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7373 (t0) REVERT: K 109 LYS cc_start: 0.8405 (mptm) cc_final: 0.7600 (tmtt) REVERT: M 38 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7359 (t0) REVERT: M 43 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7783 (ttp-110) REVERT: M 109 LYS cc_start: 0.8456 (mptm) cc_final: 0.7690 (tmtt) REVERT: N 192 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7626 (tp30) outliers start: 47 outliers final: 34 residues processed: 554 average time/residue: 0.8693 time to fit residues: 526.8429 Evaluate side-chains 581 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 540 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL 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 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 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 36 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 120 ILE 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 125 MET 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 54 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 101 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 N 153 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.120372 restraints weight = 18027.146| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 0.84 r_work: 0.3176 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19873 Z= 0.199 Angle : 0.631 9.000 26838 Z= 0.320 Chirality : 0.045 0.234 3087 Planarity : 0.004 0.030 3479 Dihedral : 10.062 59.918 2996 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.64 % Allowed : 18.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.16), residues: 2478 helix: 1.48 (0.13), residues: 1421 sheet: -2.37 (0.28), residues: 182 loop : -1.09 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 152 TYR 0.013 0.002 TYR L 95 PHE 0.010 0.002 PHE M 102 TRP 0.005 0.001 TRP K 174 HIS 0.005 0.002 HIS M 117 Details of bonding type rmsd covalent geometry : bond 0.00417 (19859) covalent geometry : angle 0.63098 (26838) hydrogen bonds : bond 0.04345 ( 1212) hydrogen bonds : angle 4.19799 ( 3846) Misc. bond : bond 0.00073 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9457.16 seconds wall clock time: 161 minutes 28.36 seconds (9688.36 seconds total)