Starting phenix.real_space_refine on Sun Aug 24 04:59:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jkb_36367/08_2025/8jkb_36367.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jkb_36367/08_2025/8jkb_36367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jkb_36367/08_2025/8jkb_36367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jkb_36367/08_2025/8jkb_36367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jkb_36367/08_2025/8jkb_36367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jkb_36367/08_2025/8jkb_36367.map" } resolution = 3.27 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 10647 2.51 5 N 3050 2.21 5 O 3332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17169 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "F" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "L" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 404 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain breaks: 1 Chain: "H" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Chain: "C" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Link IDs: {'TRANS': 50} Chain breaks: 1 Chain: "E" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Link IDs: {'TRANS': 50} Chain breaks: 1 Chain: "I" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "M" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "J" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "N" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "K" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "O" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Time building chain proxies: 4.31, per 1000 atoms: 0.25 Number of scatterers: 17169 At special positions: 0 Unit cell: (160.82, 165.98, 73.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3332 8.00 N 3050 7.00 C 10647 6.00 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=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 793.5 milliseconds Enol-peptide restraints added in 10.5 microseconds 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4154 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 41 sheets defined 16.4% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 removed outlier: 4.196A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.567A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.948A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.100A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.827A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'F' and resid 4 through 26 removed outlier: 3.869A pdb=" N ALA F 24 " --> pdb=" O ASP F 20 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 35 Processing helix chain 'L' and resid 8 through 24 removed outlier: 3.749A pdb=" N MET L 21 " --> pdb=" O GLU L 17 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN L 24 " --> pdb=" O LYS L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 44 removed outlier: 3.828A pdb=" N HIS L 44 " --> pdb=" O TYR L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 48 removed outlier: 3.882A pdb=" N ASP L 48 " --> pdb=" O ALA L 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 45 through 48' Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.645A pdb=" N THR A 174 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 174 removed outlier: 3.804A pdb=" N MET H 171 " --> pdb=" O GLU H 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 167 through 174 removed outlier: 3.740A pdb=" N MET C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 174 " --> pdb=" O GLN C 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 removed outlier: 4.150A pdb=" N MET D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'I' and resid 4 through 25 removed outlier: 3.895A pdb=" N ALA I 24 " --> pdb=" O ASP I 20 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 35 removed outlier: 3.646A pdb=" N ILE I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 24 removed outlier: 3.515A pdb=" N LYS M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET M 21 " --> pdb=" O GLU M 17 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN M 24 " --> pdb=" O LYS M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 44 Processing helix chain 'M' and resid 45 through 48 removed outlier: 3.932A pdb=" N ASP M 48 " --> pdb=" O ALA M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 45 through 48' Processing helix chain 'J' and resid 4 through 24 removed outlier: 3.903A pdb=" N ALA J 24 " --> pdb=" O ASP J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 35 removed outlier: 3.634A pdb=" N ILE J 33 " --> pdb=" O THR J 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 24 removed outlier: 3.983A pdb=" N GLU N 17 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN N 24 " --> pdb=" O LYS N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 removed outlier: 4.089A pdb=" N ALA N 33 " --> pdb=" O LYS N 29 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS N 44 " --> pdb=" O TYR N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 48 removed outlier: 3.880A pdb=" N ASP N 48 " --> pdb=" O ALA N 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 45 through 48' Processing helix chain 'K' and resid 4 through 25 removed outlier: 3.850A pdb=" N ALA K 24 " --> pdb=" O ASP K 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 35 Processing helix chain 'O' and resid 8 through 24 removed outlier: 3.586A pdb=" N LYS O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET O 21 " --> pdb=" O GLU O 17 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN O 24 " --> pdb=" O LYS O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 44 removed outlier: 3.797A pdb=" N ALA O 33 " --> pdb=" O LYS O 29 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU O 37 " --> pdb=" O ALA O 33 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS O 44 " --> pdb=" O TYR O 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.892A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.990A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.117A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.929A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.507A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.823A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 242 " --> pdb=" O CYS B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.438A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 49 through 51 removed outlier: 3.792A pdb=" N ARG F 49 " --> pdb=" O ILE F 338 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE F 338 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY F 330 " --> pdb=" O CYS F 317 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS F 317 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 60 through 63 removed outlier: 3.953A pdb=" N ALA F 60 " --> pdb=" O ALA F 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 73 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU F 70 " --> pdb=" O TRP F 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE F 81 " --> pdb=" O HIS F 91 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS F 91 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP F 83 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS F 89 " --> pdb=" O ASP F 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 104 through 105 removed outlier: 3.787A pdb=" N ALA F 104 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA F 113 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 112 " --> pdb=" O TYR F 124 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER F 122 " --> pdb=" O CYS F 114 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS F 121 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG F 137 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN F 125 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL F 135 " --> pdb=" O ASN F 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 148 through 153 removed outlier: 6.356A pdb=" N CYS F 149 " --> pdb=" O SER F 160 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER F 160 " --> pdb=" O CYS F 149 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE F 151 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL F 158 " --> pdb=" O PHE F 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 153 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE F 157 " --> pdb=" O TRP F 169 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA F 167 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS F 166 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR F 178 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASP F 170 " --> pdb=" O GLN F 176 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN F 176 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 190 through 192 removed outlier: 3.922A pdb=" N PHE F 199 " --> pdb=" O TRP F 211 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS F 209 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 229 through 232 removed outlier: 4.252A pdb=" N ALA F 231 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE F 241 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU F 252 " --> pdb=" O MET F 262 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET F 262 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP F 254 " --> pdb=" O GLU F 260 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU F 260 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 273 through 278 removed outlier: 4.460A pdb=" N SER F 275 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 285 " --> pdb=" O TRP F 297 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA F 287 " --> pdb=" O ASN F 295 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN F 295 " --> pdb=" O ALA F 287 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY F 306 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 157 through 160 Processing sheet with id=AB7, first strand: chain 'A' and resid 163 through 164 removed outlier: 3.754A pdb=" N CYS A 163 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 157 through 164 removed outlier: 3.567A pdb=" N CYS H 163 " --> pdb=" O PHE H 201 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU H 200 " --> pdb=" O ILE H 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 157 through 161 removed outlier: 3.579A pdb=" N VAL C 157 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 156 through 163 removed outlier: 3.876A pdb=" N CYS D 163 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 157 through 164 removed outlier: 3.686A pdb=" N CYS E 163 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 200 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN E 183 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 46 through 51 removed outlier: 4.021A pdb=" N ARG I 46 " --> pdb=" O ASN I 340 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN I 340 " --> pdb=" O ARG I 46 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE I 338 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR I 50 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU I 336 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY I 330 " --> pdb=" O CYS I 317 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS I 317 " --> pdb=" O GLY I 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 60 through 63 removed outlier: 3.919A pdb=" N ALA I 60 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA I 73 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU I 70 " --> pdb=" O TRP I 82 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU I 79 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA I 92 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE I 81 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN I 88 " --> pdb=" O ASP I 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 104 through 105 removed outlier: 3.676A pdb=" N CYS I 121 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG I 137 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASN I 125 " --> pdb=" O VAL I 135 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL I 135 " --> pdb=" O ASN I 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 148 through 153 removed outlier: 3.837A pdb=" N CYS I 148 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN I 156 " --> pdb=" O LEU I 152 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE I 157 " --> pdb=" O TRP I 169 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA I 167 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS I 166 " --> pdb=" O PHE I 180 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR I 178 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ASP I 170 " --> pdb=" O GLN I 176 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN I 176 " --> pdb=" O ASP I 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 190 through 192 removed outlier: 3.524A pdb=" N VAL I 200 " --> pdb=" O SER I 191 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE I 199 " --> pdb=" O TRP I 211 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU I 210 " --> pdb=" O GLN I 220 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN I 220 " --> pdb=" O LEU I 210 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 232 through 234 removed outlier: 3.582A pdb=" N PHE I 241 " --> pdb=" O PHE I 253 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS I 250 " --> pdb=" O TYR I 264 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU I 252 " --> pdb=" O MET I 262 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET I 262 " --> pdb=" O LEU I 252 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP I 254 " --> pdb=" O GLU I 260 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU I 260 " --> pdb=" O ASP I 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 273 through 278 removed outlier: 4.557A pdb=" N SER I 275 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU I 285 " --> pdb=" O TRP I 297 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA I 287 " --> pdb=" O ASN I 295 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN I 295 " --> pdb=" O ALA I 287 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS I 294 " --> pdb=" O LEU I 308 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 47 through 51 removed outlier: 4.119A pdb=" N ARG J 49 " --> pdb=" O ILE J 338 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA J 328 " --> pdb=" O LEU J 318 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU J 318 " --> pdb=" O ALA J 328 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY J 330 " --> pdb=" O SER J 316 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 60 through 63 removed outlier: 3.979A pdb=" N ALA J 60 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA J 73 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU J 70 " --> pdb=" O TRP J 82 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU J 79 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA J 92 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE J 81 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN J 88 " --> pdb=" O ASP J 83 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 100 through 105 removed outlier: 7.246A pdb=" N GLY J 115 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N CYS J 103 " --> pdb=" O ALA J 113 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA J 113 " --> pdb=" O CYS J 103 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL J 112 " --> pdb=" O TYR J 124 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS J 114 " --> pdb=" O SER J 122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER J 122 " --> pdb=" O CYS J 114 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG J 137 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN J 125 " --> pdb=" O VAL J 135 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL J 135 " --> pdb=" O ASN J 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 148 through 153 removed outlier: 3.673A pdb=" N CYS J 148 " --> pdb=" O SER J 160 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLN J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE J 157 " --> pdb=" O TRP J 169 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA J 167 " --> pdb=" O THR J 159 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS J 166 " --> pdb=" O PHE J 180 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR J 178 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP J 170 " --> pdb=" O GLN J 176 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN J 176 " --> pdb=" O ASP J 170 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 190 through 192 removed outlier: 3.808A pdb=" N PHE J 199 " --> pdb=" O TRP J 211 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS J 209 " --> pdb=" O SER J 201 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 210 " --> pdb=" O GLN J 220 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN J 220 " --> pdb=" O LEU J 210 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 229 through 234 removed outlier: 4.249A pdb=" N ALA J 231 " --> pdb=" O GLY J 244 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR J 249 " --> pdb=" O SER J 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 273 through 278 removed outlier: 4.540A pdb=" N SER J 275 " --> pdb=" O GLY J 288 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU J 285 " --> pdb=" O TRP J 297 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA J 287 " --> pdb=" O ASN J 295 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN J 295 " --> pdb=" O ALA J 287 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY J 306 " --> pdb=" O VAL J 296 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 47 through 51 removed outlier: 3.985A pdb=" N ARG K 49 " --> pdb=" O ILE K 338 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY K 330 " --> pdb=" O CYS K 317 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS K 317 " --> pdb=" O GLY K 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 60 through 63 removed outlier: 3.802A pdb=" N ALA K 60 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA K 73 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE K 81 " --> pdb=" O HIS K 91 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS K 91 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP K 83 " --> pdb=" O LYS K 89 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS K 89 " --> pdb=" O ASP K 83 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 100 through 105 removed outlier: 7.287A pdb=" N GLY K 115 " --> pdb=" O MET K 101 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N CYS K 103 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA K 113 " --> pdb=" O CYS K 103 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL K 112 " --> pdb=" O TYR K 124 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER K 122 " --> pdb=" O CYS K 114 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE K 123 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN K 125 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG K 134 " --> pdb=" O ASN K 125 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 148 through 153 removed outlier: 3.872A pdb=" N CYS K 148 " --> pdb=" O SER K 160 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE K 157 " --> pdb=" O TRP K 169 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA K 167 " --> pdb=" O THR K 159 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS K 166 " --> pdb=" O PHE K 180 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR K 178 " --> pdb=" O LEU K 168 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ASP K 170 " --> pdb=" O GLN K 176 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN K 176 " --> pdb=" O ASP K 170 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 190 through 192 removed outlier: 3.556A pdb=" N SER K 191 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL K 200 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE K 199 " --> pdb=" O TRP K 211 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS K 209 " --> pdb=" O SER K 201 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 229 through 234 removed outlier: 4.044A pdb=" N ALA K 231 " --> pdb=" O GLY K 244 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU K 252 " --> pdb=" O MET K 262 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET K 262 " --> pdb=" O LEU K 252 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 273 through 278 removed outlier: 4.555A pdb=" N SER K 275 " --> pdb=" O GLY K 288 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU K 285 " --> pdb=" O TRP K 297 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA K 287 " --> pdb=" O ASN K 295 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN K 295 " --> pdb=" O ALA K 287 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS K 294 " --> pdb=" O LEU K 308 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY K 306 " --> pdb=" O VAL K 296 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1341 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: 2.86 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3240 1.32 - 1.45: 4351 1.45 - 1.57: 9675 1.57 - 1.69: 3 1.69 - 1.81: 195 Bond restraints: 17464 Sorted by residual: bond pdb=" N ASN F 293 " pdb=" CA ASN F 293 " ideal model delta sigma weight residual 1.457 1.495 -0.039 1.53e-02 4.27e+03 6.40e+00 bond pdb=" C TYR B 289 " pdb=" O TYR B 289 " ideal model delta sigma weight residual 1.234 1.203 0.031 1.26e-02 6.30e+03 5.87e+00 bond pdb=" CA ASP I 290 " pdb=" CB ASP I 290 " ideal model delta sigma weight residual 1.530 1.494 0.036 1.51e-02 4.39e+03 5.63e+00 bond pdb=" CA PHE B 292 " pdb=" C PHE B 292 " ideal model delta sigma weight residual 1.523 1.557 -0.034 1.45e-02 4.76e+03 5.55e+00 bond pdb=" CA ASP B 290 " pdb=" CB ASP B 290 " ideal model delta sigma weight residual 1.531 1.493 0.038 1.69e-02 3.50e+03 5.07e+00 ... (remaining 17459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 23202 2.08 - 4.16: 358 4.16 - 6.24: 61 6.24 - 8.32: 10 8.32 - 10.40: 5 Bond angle restraints: 23636 Sorted by residual: angle pdb=" N ASN B 293 " pdb=" CA ASN B 293 " pdb=" C ASN B 293 " ideal model delta sigma weight residual 108.19 116.67 -8.48 1.29e+00 6.01e-01 4.33e+01 angle pdb=" N ARG J 219 " pdb=" CA ARG J 219 " pdb=" C ARG J 219 " ideal model delta sigma weight residual 112.38 120.30 -7.92 1.22e+00 6.72e-01 4.22e+01 angle pdb=" N ALA G 10 " pdb=" CA ALA G 10 " pdb=" C ALA G 10 " ideal model delta sigma weight residual 111.28 104.66 6.62 1.09e+00 8.42e-01 3.69e+01 angle pdb=" N ASN F 293 " pdb=" CA ASN F 293 " pdb=" C ASN F 293 " ideal model delta sigma weight residual 108.34 115.95 -7.61 1.31e+00 5.83e-01 3.38e+01 angle pdb=" N GLU G 17 " pdb=" CA GLU G 17 " pdb=" C GLU G 17 " ideal model delta sigma weight residual 111.36 117.12 -5.76 1.09e+00 8.42e-01 2.79e+01 ... (remaining 23631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 9534 16.96 - 33.93: 722 33.93 - 50.89: 155 50.89 - 67.86: 32 67.86 - 84.82: 18 Dihedral angle restraints: 10461 sinusoidal: 4057 harmonic: 6404 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PHE J 234 " pdb=" C PHE J 234 " pdb=" N PHE J 235 " pdb=" CA PHE J 235 " ideal model delta harmonic sigma weight residual 180.00 162.44 17.56 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 10458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1922 0.043 - 0.086: 529 0.086 - 0.129: 201 0.129 - 0.172: 23 0.172 - 0.215: 2 Chirality restraints: 2677 Sorted by residual: chirality pdb=" CA ARG J 219 " pdb=" N ARG J 219 " pdb=" C ARG J 219 " pdb=" CB ARG J 219 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA MET H 171 " pdb=" N MET H 171 " pdb=" C MET H 171 " pdb=" CB MET H 171 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE L 9 " pdb=" N ILE L 9 " pdb=" C ILE L 9 " pdb=" CB ILE L 9 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 2674 not shown) Planarity restraints: 3060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER G 8 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C SER G 8 " 0.069 2.00e-02 2.50e+03 pdb=" O SER G 8 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE G 9 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP M 48 " 0.056 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO M 49 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO M 49 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO M 49 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 235 " -0.014 2.00e-02 2.50e+03 1.92e-02 6.46e+00 pdb=" CG PHE K 235 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE K 235 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE K 235 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE K 235 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE K 235 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 235 " -0.000 2.00e-02 2.50e+03 ... (remaining 3057 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 465 2.69 - 3.25: 15786 3.25 - 3.80: 23756 3.80 - 4.35: 30461 4.35 - 4.90: 53275 Nonbonded interactions: 123743 Sorted by model distance: nonbonded pdb=" OE2 GLU J 260 " pdb=" OG1 THR J 263 " model vdw 2.142 3.040 nonbonded pdb=" O ALA F 56 " pdb=" OG SER F 334 " model vdw 2.147 3.040 nonbonded pdb=" O GLN D 170 " pdb=" OG1 THR D 174 " model vdw 2.165 3.040 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.203 3.040 nonbonded pdb=" OE2 GLU I 260 " pdb=" OG1 THR I 263 " model vdw 2.214 3.040 ... (remaining 123738 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 153 through 187 or resid 198 through 211)) selection = chain 'C' selection = (chain 'D' and (resid 153 through 187 or resid 198 through 211)) selection = (chain 'E' and (resid 153 through 187 or resid 198 through 211)) selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.870 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 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 : 0.004 0.091 17464 Z= 0.193 Angle : 0.674 10.398 23636 Z= 0.383 Chirality : 0.046 0.215 2677 Planarity : 0.004 0.085 3060 Dihedral : 13.374 84.823 6307 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.16 % Allowed : 1.18 % Favored : 98.66 % 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: -1.95 (0.17), residues: 2180 helix: 0.85 (0.30), residues: 315 sheet: -1.10 (0.19), residues: 743 loop : -2.10 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 49 TYR 0.035 0.002 TYR I 105 PHE 0.044 0.002 PHE K 235 TRP 0.023 0.002 TRP K 63 HIS 0.006 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00384 (17464) covalent geometry : angle 0.67445 (23636) hydrogen bonds : bond 0.26094 ( 476) hydrogen bonds : angle 8.06052 ( 1341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 388 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 311 HIS cc_start: 0.6292 (m-70) cc_final: 0.5528 (m-70) outliers start: 3 outliers final: 1 residues processed: 389 average time/residue: 0.1818 time to fit residues: 97.9132 Evaluate side-chains 230 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 13 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 0.0570 chunk 77 optimal weight: 9.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 142 HIS F 44 GLN F 91 HIS F 142 HIS F 237 ASN ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 GLN L 44 HIS A 162 GLN C 211 ASN ** I 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN N 24 ASN N 44 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.076370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048221 restraints weight = 74089.144| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 5.40 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17464 Z= 0.212 Angle : 0.683 10.260 23636 Z= 0.358 Chirality : 0.044 0.144 2677 Planarity : 0.006 0.143 3060 Dihedral : 4.928 55.555 2384 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.66 % Allowed : 12.10 % Favored : 86.23 % 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: -1.75 (0.17), residues: 2180 helix: 0.84 (0.29), residues: 309 sheet: -0.79 (0.19), residues: 714 loop : -2.01 (0.16), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 214 TYR 0.027 0.002 TYR J 111 PHE 0.015 0.002 PHE G 61 TRP 0.014 0.002 TRP D 179 HIS 0.006 0.001 HIS H 156 Details of bonding type rmsd covalent geometry : bond 0.00477 (17464) covalent geometry : angle 0.68337 (23636) hydrogen bonds : bond 0.04726 ( 476) hydrogen bonds : angle 5.51215 ( 1341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 ASP cc_start: 0.8911 (t0) cc_final: 0.8534 (p0) REVERT: B 325 MET cc_start: 0.9273 (mtp) cc_final: 0.8760 (mtp) REVERT: F 111 TYR cc_start: 0.8953 (m-80) cc_final: 0.8376 (m-80) REVERT: F 339 TRP cc_start: 0.8889 (m100) cc_final: 0.7935 (m-10) REVERT: L 21 MET cc_start: 0.8901 (tmm) cc_final: 0.8641 (tmm) REVERT: H 164 GLN cc_start: 0.8650 (mt0) cc_final: 0.8298 (tp40) REVERT: D 180 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8744 (mmmt) REVERT: E 182 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8237 (mm-30) REVERT: I 57 LYS cc_start: 0.9221 (mtmm) cc_final: 0.8929 (mtpp) REVERT: I 127 LYS cc_start: 0.9545 (mmtp) cc_final: 0.9235 (tppt) REVERT: I 153 ASP cc_start: 0.9000 (t0) cc_final: 0.8534 (p0) REVERT: I 337 LYS cc_start: 0.8651 (mmtm) cc_final: 0.8317 (mmmm) REVERT: M 21 MET cc_start: 0.9077 (tmm) cc_final: 0.8829 (ppp) REVERT: M 32 LYS cc_start: 0.9818 (pttt) cc_final: 0.9447 (pttt) REVERT: J 153 ASP cc_start: 0.8868 (t0) cc_final: 0.8430 (p0) REVERT: J 311 HIS cc_start: 0.8521 (m-70) cc_final: 0.7223 (m-70) REVERT: J 325 MET cc_start: 0.9220 (ptm) cc_final: 0.8919 (ptp) REVERT: J 337 LYS cc_start: 0.8613 (mttm) cc_final: 0.8147 (ptpt) REVERT: K 127 LYS cc_start: 0.9511 (mmtp) cc_final: 0.9275 (tppt) REVERT: K 153 ASP cc_start: 0.8884 (t0) cc_final: 0.8506 (p0) REVERT: K 325 MET cc_start: 0.8857 (mtp) cc_final: 0.8469 (mtp) REVERT: K 337 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8241 (mmmm) outliers start: 31 outliers final: 15 residues processed: 271 average time/residue: 0.1885 time to fit residues: 70.4317 Evaluate side-chains 239 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 180 LYS Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain J residue 142 HIS Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 214 ARG Chi-restraints excluded: chain O residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 66 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** I 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.074500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.046245 restraints weight = 77313.392| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 5.36 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17464 Z= 0.245 Angle : 0.669 11.670 23636 Z= 0.351 Chirality : 0.044 0.147 2677 Planarity : 0.005 0.100 3060 Dihedral : 4.912 55.556 2384 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.36 % Allowed : 13.93 % Favored : 83.72 % 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: -1.76 (0.17), residues: 2180 helix: 0.29 (0.27), residues: 329 sheet: -0.72 (0.19), residues: 716 loop : -1.95 (0.16), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 129 TYR 0.020 0.002 TYR J 111 PHE 0.017 0.002 PHE K 241 TRP 0.015 0.002 TRP J 297 HIS 0.010 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00548 (17464) covalent geometry : angle 0.66940 (23636) hydrogen bonds : bond 0.04722 ( 476) hydrogen bonds : angle 5.29031 ( 1341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 ASP cc_start: 0.9018 (t0) cc_final: 0.8621 (p0) REVERT: B 325 MET cc_start: 0.9255 (mtp) cc_final: 0.8672 (mtp) REVERT: G 32 LYS cc_start: 0.9856 (OUTLIER) cc_final: 0.9652 (pttm) REVERT: F 61 MET cc_start: 0.8758 (ppp) cc_final: 0.8511 (ppp) REVERT: F 111 TYR cc_start: 0.8933 (m-80) cc_final: 0.8470 (m-80) REVERT: F 153 ASP cc_start: 0.8979 (t0) cc_final: 0.8470 (p0) REVERT: F 325 MET cc_start: 0.9415 (mtm) cc_final: 0.8932 (mtp) REVERT: F 337 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8585 (mmmm) REVERT: F 339 TRP cc_start: 0.9018 (m100) cc_final: 0.8243 (m100) REVERT: L 21 MET cc_start: 0.8886 (tmm) cc_final: 0.8594 (tmm) REVERT: H 167 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8215 (pm20) REVERT: D 175 MET cc_start: 0.9224 (tpp) cc_final: 0.8910 (tpp) REVERT: D 182 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8558 (mm-30) REVERT: E 180 LYS cc_start: 0.9448 (mtpp) cc_final: 0.9192 (mtpp) REVERT: I 57 LYS cc_start: 0.9315 (mtmm) cc_final: 0.9005 (mtpp) REVERT: I 127 LYS cc_start: 0.9537 (mmtp) cc_final: 0.9222 (tppt) REVERT: I 145 TYR cc_start: 0.9308 (p90) cc_final: 0.9103 (p90) REVERT: I 153 ASP cc_start: 0.9048 (t0) cc_final: 0.8617 (p0) REVERT: I 337 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8321 (mmmm) REVERT: M 21 MET cc_start: 0.9070 (tmm) cc_final: 0.8841 (ppp) REVERT: J 153 ASP cc_start: 0.8926 (t0) cc_final: 0.8503 (p0) REVERT: J 188 MET cc_start: 0.9172 (mtm) cc_final: 0.8787 (mtm) REVERT: J 292 PHE cc_start: 0.9357 (m-80) cc_final: 0.8925 (m-80) REVERT: J 325 MET cc_start: 0.9317 (ptm) cc_final: 0.8968 (ptp) REVERT: J 337 LYS cc_start: 0.8621 (mttm) cc_final: 0.8128 (mttm) REVERT: K 78 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8046 (ttpt) REVERT: K 127 LYS cc_start: 0.9512 (mmtp) cc_final: 0.9253 (tppt) REVERT: K 153 ASP cc_start: 0.9066 (t0) cc_final: 0.8643 (p0) REVERT: K 325 MET cc_start: 0.8910 (mtp) cc_final: 0.8531 (mtp) REVERT: K 337 LYS cc_start: 0.8800 (mmtm) cc_final: 0.8284 (mmmm) outliers start: 44 outliers final: 29 residues processed: 260 average time/residue: 0.1778 time to fit residues: 64.5371 Evaluate side-chains 239 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain J residue 142 HIS Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 78 LYS Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 24 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 206 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 175 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN I 311 HIS J 88 ASN K 88 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.074252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.045910 restraints weight = 76434.270| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 5.35 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17464 Z= 0.191 Angle : 0.630 13.250 23636 Z= 0.327 Chirality : 0.043 0.147 2677 Planarity : 0.004 0.066 3060 Dihedral : 4.728 54.648 2384 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.57 % Allowed : 15.37 % Favored : 82.06 % 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: -1.66 (0.17), residues: 2180 helix: 0.19 (0.27), residues: 329 sheet: -0.57 (0.20), residues: 716 loop : -1.87 (0.16), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 197 TYR 0.013 0.001 TYR F 145 PHE 0.015 0.001 PHE K 241 TRP 0.012 0.001 TRP J 297 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00429 (17464) covalent geometry : angle 0.63048 (23636) hydrogen bonds : bond 0.04031 ( 476) hydrogen bonds : angle 5.07521 ( 1341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 ASP cc_start: 0.9014 (t0) cc_final: 0.8621 (p0) REVERT: B 188 MET cc_start: 0.7544 (mpp) cc_final: 0.7227 (mpp) REVERT: B 325 MET cc_start: 0.9241 (mtp) cc_final: 0.8770 (mmm) REVERT: F 12 GLU cc_start: 0.9733 (pp20) cc_final: 0.9447 (pp20) REVERT: F 111 TYR cc_start: 0.8943 (m-80) cc_final: 0.8512 (m-80) REVERT: F 153 ASP cc_start: 0.8981 (t0) cc_final: 0.8468 (p0) REVERT: F 325 MET cc_start: 0.9392 (mtm) cc_final: 0.8906 (mtp) REVERT: F 337 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8749 (mmmt) REVERT: F 339 TRP cc_start: 0.9099 (m100) cc_final: 0.8396 (m100) REVERT: L 21 MET cc_start: 0.8680 (tmm) cc_final: 0.8306 (tmm) REVERT: H 167 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: D 175 MET cc_start: 0.9355 (tpp) cc_final: 0.8993 (tpp) REVERT: I 57 LYS cc_start: 0.9304 (mtmm) cc_final: 0.9017 (mtpp) REVERT: I 127 LYS cc_start: 0.9507 (mmtp) cc_final: 0.9182 (tppt) REVERT: I 153 ASP cc_start: 0.9000 (t0) cc_final: 0.8566 (p0) REVERT: I 183 HIS cc_start: 0.8734 (OUTLIER) cc_final: 0.8420 (t70) REVERT: I 337 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8332 (mmmm) REVERT: M 21 MET cc_start: 0.9058 (tmm) cc_final: 0.8827 (ppp) REVERT: J 153 ASP cc_start: 0.8896 (t0) cc_final: 0.8455 (p0) REVERT: J 188 MET cc_start: 0.9147 (mtm) cc_final: 0.8804 (mtm) REVERT: J 325 MET cc_start: 0.9246 (ptm) cc_final: 0.8906 (ptp) REVERT: J 337 LYS cc_start: 0.8625 (mttm) cc_final: 0.8012 (mttm) REVERT: K 127 LYS cc_start: 0.9518 (mmtp) cc_final: 0.9254 (tppt) REVERT: K 153 ASP cc_start: 0.9021 (t0) cc_final: 0.8631 (p0) REVERT: K 188 MET cc_start: 0.8848 (mmm) cc_final: 0.8603 (mmp) REVERT: K 325 MET cc_start: 0.8808 (mtp) cc_final: 0.8421 (mtp) REVERT: K 337 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8238 (mmmm) REVERT: O 21 MET cc_start: 0.9474 (tmm) cc_final: 0.9244 (ppp) outliers start: 48 outliers final: 28 residues processed: 259 average time/residue: 0.1497 time to fit residues: 54.7311 Evaluate side-chains 236 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain J residue 142 HIS Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 24 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 201 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 210 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN N 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.074301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.046115 restraints weight = 75398.181| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 5.31 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17464 Z= 0.162 Angle : 0.618 10.459 23636 Z= 0.320 Chirality : 0.043 0.167 2677 Planarity : 0.004 0.059 3060 Dihedral : 4.555 54.389 2384 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.68 % Allowed : 16.71 % Favored : 80.61 % 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: -1.59 (0.17), residues: 2180 helix: 0.02 (0.27), residues: 334 sheet: -0.48 (0.19), residues: 741 loop : -1.82 (0.16), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.006 0.001 TYR M 40 PHE 0.015 0.001 PHE K 241 TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00367 (17464) covalent geometry : angle 0.61826 (23636) hydrogen bonds : bond 0.03803 ( 476) hydrogen bonds : angle 4.95138 ( 1341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 GLU cc_start: 0.9729 (pp20) cc_final: 0.9469 (pp20) REVERT: B 153 ASP cc_start: 0.8994 (t0) cc_final: 0.8579 (p0) REVERT: B 188 MET cc_start: 0.7649 (mpp) cc_final: 0.7399 (mpp) REVERT: B 325 MET cc_start: 0.9238 (mtp) cc_final: 0.8764 (mmm) REVERT: F 111 TYR cc_start: 0.8976 (m-80) cc_final: 0.8560 (m-80) REVERT: F 153 ASP cc_start: 0.8966 (t0) cc_final: 0.8480 (p0) REVERT: F 325 MET cc_start: 0.9367 (mtm) cc_final: 0.8882 (mtp) REVERT: F 337 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8441 (mmmm) REVERT: F 339 TRP cc_start: 0.9109 (m100) cc_final: 0.8427 (m100) REVERT: L 21 MET cc_start: 0.8598 (tmm) cc_final: 0.8344 (tmm) REVERT: L 47 GLU cc_start: 0.9275 (mp0) cc_final: 0.8975 (pm20) REVERT: A 165 GLU cc_start: 0.9324 (tm-30) cc_final: 0.8935 (pm20) REVERT: H 167 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8280 (pm20) REVERT: C 175 MET cc_start: 0.9446 (tpp) cc_final: 0.9168 (tpp) REVERT: D 175 MET cc_start: 0.9409 (tpp) cc_final: 0.8986 (tpp) REVERT: E 175 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9149 (mmm) REVERT: I 57 LYS cc_start: 0.9308 (mtmm) cc_final: 0.9006 (mtpp) REVERT: I 101 MET cc_start: 0.9125 (ptp) cc_final: 0.8823 (pmm) REVERT: I 127 LYS cc_start: 0.9516 (mmtp) cc_final: 0.9197 (tppt) REVERT: I 153 ASP cc_start: 0.8990 (t0) cc_final: 0.8639 (p0) REVERT: I 183 HIS cc_start: 0.8745 (OUTLIER) cc_final: 0.8408 (t70) REVERT: I 337 LYS cc_start: 0.8746 (mmtm) cc_final: 0.8323 (mmmm) REVERT: M 21 MET cc_start: 0.9059 (tmm) cc_final: 0.8839 (ppp) REVERT: J 153 ASP cc_start: 0.8938 (t0) cc_final: 0.8572 (p0) REVERT: J 188 MET cc_start: 0.9160 (mtm) cc_final: 0.8528 (mpp) REVERT: J 325 MET cc_start: 0.9176 (ptm) cc_final: 0.8818 (ptp) REVERT: J 337 LYS cc_start: 0.8633 (mttm) cc_final: 0.8065 (mttm) REVERT: K 127 LYS cc_start: 0.9519 (mmtp) cc_final: 0.9278 (tppt) REVERT: K 153 ASP cc_start: 0.9025 (t0) cc_final: 0.8626 (p0) REVERT: K 325 MET cc_start: 0.8723 (mtp) cc_final: 0.8219 (mtp) REVERT: K 337 LYS cc_start: 0.8780 (mmtm) cc_final: 0.8275 (mmmm) outliers start: 50 outliers final: 31 residues processed: 262 average time/residue: 0.1422 time to fit residues: 52.6507 Evaluate side-chains 240 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 142 HIS Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 24 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 73 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.073415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.045224 restraints weight = 76273.213| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 5.31 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17464 Z= 0.213 Angle : 0.669 13.705 23636 Z= 0.347 Chirality : 0.043 0.153 2677 Planarity : 0.004 0.055 3060 Dihedral : 4.627 55.565 2384 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.11 % Allowed : 16.87 % Favored : 80.02 % 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: -1.67 (0.17), residues: 2180 helix: -0.30 (0.28), residues: 334 sheet: -0.47 (0.19), residues: 743 loop : -1.83 (0.16), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 13 TYR 0.030 0.002 TYR B 145 PHE 0.014 0.001 PHE K 241 TRP 0.012 0.001 TRP K 339 HIS 0.006 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00479 (17464) covalent geometry : angle 0.66909 (23636) hydrogen bonds : bond 0.04194 ( 476) hydrogen bonds : angle 5.03135 ( 1341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 225 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 LYS cc_start: 0.9899 (tptp) cc_final: 0.9689 (mttt) REVERT: B 153 ASP cc_start: 0.9043 (t0) cc_final: 0.8645 (p0) REVERT: B 325 MET cc_start: 0.9242 (mtp) cc_final: 0.8767 (mmm) REVERT: G 47 GLU cc_start: 0.9220 (mp0) cc_final: 0.8815 (pm20) REVERT: F 111 TYR cc_start: 0.9015 (m-80) cc_final: 0.8564 (m-80) REVERT: F 142 HIS cc_start: 0.8784 (OUTLIER) cc_final: 0.8033 (p90) REVERT: F 153 ASP cc_start: 0.9025 (t0) cc_final: 0.8498 (p0) REVERT: F 325 MET cc_start: 0.9362 (mtm) cc_final: 0.8871 (mtp) REVERT: F 337 LYS cc_start: 0.9042 (mmmm) cc_final: 0.8521 (mmmm) REVERT: F 339 TRP cc_start: 0.9153 (m100) cc_final: 0.8872 (m-10) REVERT: L 21 MET cc_start: 0.8569 (tmm) cc_final: 0.8280 (tmm) REVERT: A 182 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8475 (mm-30) REVERT: H 167 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: H 175 MET cc_start: 0.9494 (tpp) cc_final: 0.9266 (tpp) REVERT: D 175 MET cc_start: 0.9461 (tpp) cc_final: 0.9132 (tpp) REVERT: I 57 LYS cc_start: 0.9339 (mtmm) cc_final: 0.9011 (mtpp) REVERT: I 127 LYS cc_start: 0.9495 (mmtp) cc_final: 0.9173 (tppt) REVERT: I 153 ASP cc_start: 0.9069 (t0) cc_final: 0.8643 (p0) REVERT: I 183 HIS cc_start: 0.8758 (OUTLIER) cc_final: 0.8501 (t70) REVERT: I 264 TYR cc_start: 0.8730 (m-80) cc_final: 0.8347 (m-80) REVERT: I 337 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8371 (mmmm) REVERT: M 14 LYS cc_start: 0.9658 (tppt) cc_final: 0.9458 (tppt) REVERT: M 17 GLU cc_start: 0.9649 (tm-30) cc_final: 0.9277 (pt0) REVERT: M 21 MET cc_start: 0.9016 (tmm) cc_final: 0.8810 (ppp) REVERT: J 153 ASP cc_start: 0.9016 (t0) cc_final: 0.8595 (p0) REVERT: J 188 MET cc_start: 0.9168 (mtm) cc_final: 0.8544 (mpp) REVERT: J 292 PHE cc_start: 0.9389 (m-80) cc_final: 0.8936 (m-10) REVERT: J 325 MET cc_start: 0.9187 (ptm) cc_final: 0.8843 (mpp) REVERT: J 337 LYS cc_start: 0.8705 (mttm) cc_final: 0.8115 (mttm) REVERT: K 71 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8361 (m) REVERT: K 127 LYS cc_start: 0.9513 (mmtp) cc_final: 0.9260 (tppt) REVERT: K 153 ASP cc_start: 0.9058 (t0) cc_final: 0.8660 (p0) REVERT: K 325 MET cc_start: 0.8694 (mtp) cc_final: 0.8291 (mtp) REVERT: K 337 LYS cc_start: 0.8802 (mmtm) cc_final: 0.8273 (mmmm) outliers start: 58 outliers final: 39 residues processed: 262 average time/residue: 0.1550 time to fit residues: 57.2098 Evaluate side-chains 245 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 24 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 160 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.074208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.046298 restraints weight = 76452.251| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 5.32 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17464 Z= 0.134 Angle : 0.665 14.133 23636 Z= 0.341 Chirality : 0.043 0.137 2677 Planarity : 0.004 0.055 3060 Dihedral : 4.427 54.825 2384 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.62 % Allowed : 17.94 % Favored : 79.43 % 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: -1.56 (0.17), residues: 2180 helix: -0.59 (0.27), residues: 334 sheet: -0.09 (0.20), residues: 706 loop : -1.83 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 13 TYR 0.015 0.001 TYR I 264 PHE 0.014 0.001 PHE K 241 TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00305 (17464) covalent geometry : angle 0.66523 (23636) hydrogen bonds : bond 0.03711 ( 476) hydrogen bonds : angle 4.94643 ( 1341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 LYS cc_start: 0.9902 (tptp) cc_final: 0.9696 (mttt) REVERT: B 153 ASP cc_start: 0.8989 (t0) cc_final: 0.8551 (p0) REVERT: B 262 MET cc_start: 0.8593 (mpp) cc_final: 0.8351 (mpp) REVERT: B 325 MET cc_start: 0.9208 (mtp) cc_final: 0.8738 (mmm) REVERT: F 61 MET cc_start: 0.8693 (ppp) cc_final: 0.8335 (ppp) REVERT: F 111 TYR cc_start: 0.8982 (m-80) cc_final: 0.8589 (m-80) REVERT: F 124 TYR cc_start: 0.9265 (m-80) cc_final: 0.8941 (m-80) REVERT: F 142 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.7881 (p90) REVERT: F 153 ASP cc_start: 0.9009 (t0) cc_final: 0.8484 (p0) REVERT: F 217 MET cc_start: 0.8904 (mmm) cc_final: 0.8698 (mmm) REVERT: F 325 MET cc_start: 0.9334 (mtm) cc_final: 0.8874 (mtp) REVERT: F 337 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8509 (mmmm) REVERT: F 339 TRP cc_start: 0.9164 (m100) cc_final: 0.8952 (m-10) REVERT: L 21 MET cc_start: 0.8477 (tmm) cc_final: 0.7981 (tmm) REVERT: H 167 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8281 (pm20) REVERT: C 182 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8386 (mm-30) REVERT: I 57 LYS cc_start: 0.9310 (mtmm) cc_final: 0.9011 (mtpp) REVERT: I 101 MET cc_start: 0.9151 (ptp) cc_final: 0.8853 (pmm) REVERT: I 127 LYS cc_start: 0.9496 (mmtp) cc_final: 0.9167 (tppt) REVERT: I 153 ASP cc_start: 0.9014 (t0) cc_final: 0.8596 (p0) REVERT: I 183 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.8374 (t70) REVERT: I 188 MET cc_start: 0.9130 (mmp) cc_final: 0.8541 (mmp) REVERT: I 264 TYR cc_start: 0.8653 (m-80) cc_final: 0.8209 (m-80) REVERT: I 321 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8368 (p) REVERT: I 337 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8324 (mmmm) REVERT: M 21 MET cc_start: 0.9037 (tmm) cc_final: 0.8805 (ppp) REVERT: J 153 ASP cc_start: 0.8967 (t0) cc_final: 0.8553 (p0) REVERT: J 188 MET cc_start: 0.9144 (mtm) cc_final: 0.8519 (mpp) REVERT: J 292 PHE cc_start: 0.9416 (m-80) cc_final: 0.8940 (m-10) REVERT: J 325 MET cc_start: 0.9162 (ptm) cc_final: 0.8810 (mpp) REVERT: J 337 LYS cc_start: 0.8644 (mttm) cc_final: 0.8075 (mttm) REVERT: K 71 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8422 (p) REVERT: K 127 LYS cc_start: 0.9517 (mmtp) cc_final: 0.9258 (tppt) REVERT: K 153 ASP cc_start: 0.9048 (t0) cc_final: 0.8651 (p0) REVERT: K 188 MET cc_start: 0.9075 (mmp) cc_final: 0.8727 (mmp) REVERT: K 325 MET cc_start: 0.8638 (mtp) cc_final: 0.8310 (mtp) REVERT: K 337 LYS cc_start: 0.8745 (mmtm) cc_final: 0.8221 (mmmm) outliers start: 49 outliers final: 35 residues processed: 264 average time/residue: 0.1518 time to fit residues: 57.0910 Evaluate side-chains 250 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 321 THR Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain O residue 24 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 8 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 101 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 97 optimal weight: 0.0030 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.073280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.045098 restraints weight = 76328.961| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 5.30 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17464 Z= 0.195 Angle : 0.700 13.767 23636 Z= 0.361 Chirality : 0.043 0.139 2677 Planarity : 0.004 0.055 3060 Dihedral : 4.546 55.528 2384 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.79 % Allowed : 18.43 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.56 (0.17), residues: 2180 helix: -0.60 (0.28), residues: 334 sheet: -0.25 (0.19), residues: 741 loop : -1.73 (0.16), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 13 TYR 0.014 0.001 TYR I 264 PHE 0.014 0.001 PHE K 241 TRP 0.018 0.001 TRP B 339 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00440 (17464) covalent geometry : angle 0.70035 (23636) hydrogen bonds : bond 0.04089 ( 476) hydrogen bonds : angle 5.08310 ( 1341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 LYS cc_start: 0.9911 (tptp) cc_final: 0.9698 (mttt) REVERT: B 153 ASP cc_start: 0.9038 (t0) cc_final: 0.8610 (p0) REVERT: B 217 MET cc_start: 0.8365 (ppp) cc_final: 0.8098 (ppp) REVERT: B 262 MET cc_start: 0.8631 (mpp) cc_final: 0.8356 (mpp) REVERT: B 325 MET cc_start: 0.9264 (mtp) cc_final: 0.8745 (mmm) REVERT: F 61 MET cc_start: 0.8630 (ppp) cc_final: 0.8395 (ppp) REVERT: F 111 TYR cc_start: 0.8996 (m-80) cc_final: 0.8573 (m-80) REVERT: F 142 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.8100 (p90) REVERT: F 153 ASP cc_start: 0.9022 (t0) cc_final: 0.8482 (p0) REVERT: F 325 MET cc_start: 0.9344 (mtm) cc_final: 0.8857 (mtp) REVERT: F 337 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8562 (mmmm) REVERT: L 21 MET cc_start: 0.8432 (tmm) cc_final: 0.8111 (tmm) REVERT: L 38 MET cc_start: 0.9888 (ppp) cc_final: 0.9442 (pmm) REVERT: H 175 MET cc_start: 0.9553 (mmm) cc_final: 0.9329 (tpp) REVERT: C 182 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8366 (mm-30) REVERT: E 175 MET cc_start: 0.9436 (tpp) cc_final: 0.8617 (mpp) REVERT: I 57 LYS cc_start: 0.9341 (mtmm) cc_final: 0.8989 (mtpp) REVERT: I 127 LYS cc_start: 0.9475 (mmtp) cc_final: 0.9160 (tppt) REVERT: I 153 ASP cc_start: 0.9044 (t0) cc_final: 0.8620 (p0) REVERT: I 183 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8493 (t70) REVERT: I 264 TYR cc_start: 0.8659 (m-80) cc_final: 0.8226 (m-80) REVERT: I 321 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8312 (p) REVERT: I 337 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8348 (mmmm) REVERT: M 14 LYS cc_start: 0.9664 (tppt) cc_final: 0.9457 (tppt) REVERT: M 17 GLU cc_start: 0.9599 (tm-30) cc_final: 0.9201 (pt0) REVERT: J 12 GLU cc_start: 0.9600 (pp20) cc_final: 0.9247 (pp20) REVERT: J 153 ASP cc_start: 0.8970 (t0) cc_final: 0.8546 (p0) REVERT: J 188 MET cc_start: 0.9183 (mtm) cc_final: 0.8549 (mpp) REVERT: J 292 PHE cc_start: 0.9422 (m-80) cc_final: 0.9209 (m-80) REVERT: J 325 MET cc_start: 0.9190 (ptm) cc_final: 0.8793 (mpp) REVERT: J 337 LYS cc_start: 0.8676 (mttm) cc_final: 0.8096 (mttm) REVERT: N 47 GLU cc_start: 0.8712 (pm20) cc_final: 0.8404 (pm20) REVERT: K 61 MET cc_start: 0.8594 (ppp) cc_final: 0.8045 (ppp) REVERT: K 71 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8269 (m) REVERT: K 153 ASP cc_start: 0.9048 (t0) cc_final: 0.8638 (p0) REVERT: K 325 MET cc_start: 0.8696 (mtp) cc_final: 0.8318 (mtp) REVERT: K 337 LYS cc_start: 0.8767 (mmtm) cc_final: 0.8236 (mmmm) outliers start: 52 outliers final: 40 residues processed: 257 average time/residue: 0.1621 time to fit residues: 58.4956 Evaluate side-chains 248 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 321 THR Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain O residue 24 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 57 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 130 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.074016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.045767 restraints weight = 75349.890| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 5.28 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17464 Z= 0.143 Angle : 0.736 17.348 23636 Z= 0.372 Chirality : 0.044 0.180 2677 Planarity : 0.004 0.054 3060 Dihedral : 4.453 55.667 2384 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.20 % Allowed : 19.87 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.47 (0.17), residues: 2180 helix: -0.79 (0.28), residues: 333 sheet: 0.11 (0.20), residues: 704 loop : -1.78 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 13 TYR 0.014 0.001 TYR I 264 PHE 0.013 0.001 PHE K 241 TRP 0.018 0.001 TRP B 339 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00329 (17464) covalent geometry : angle 0.73625 (23636) hydrogen bonds : bond 0.03785 ( 476) hydrogen bonds : angle 5.06619 ( 1341) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 217 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 ASP cc_start: 0.9011 (t0) cc_final: 0.8578 (p0) REVERT: B 262 MET cc_start: 0.8681 (mpp) cc_final: 0.8397 (mpp) REVERT: B 325 MET cc_start: 0.9258 (mtp) cc_final: 0.8289 (ttt) REVERT: F 61 MET cc_start: 0.8602 (ppp) cc_final: 0.8392 (ppp) REVERT: F 111 TYR cc_start: 0.8977 (m-80) cc_final: 0.8552 (m-80) REVERT: F 124 TYR cc_start: 0.9278 (m-80) cc_final: 0.8970 (m-80) REVERT: F 142 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.8029 (p90) REVERT: F 153 ASP cc_start: 0.9002 (t0) cc_final: 0.8468 (p0) REVERT: F 325 MET cc_start: 0.9329 (mtm) cc_final: 0.8844 (mtp) REVERT: F 337 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8562 (mmmm) REVERT: L 21 MET cc_start: 0.8431 (tmm) cc_final: 0.8026 (tmm) REVERT: A 182 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8460 (mm-30) REVERT: H 175 MET cc_start: 0.9552 (mmm) cc_final: 0.9260 (tpp) REVERT: C 182 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8393 (mm-30) REVERT: I 57 LYS cc_start: 0.9311 (mtmm) cc_final: 0.9000 (mtpp) REVERT: I 101 MET cc_start: 0.9164 (ptp) cc_final: 0.8856 (pmm) REVERT: I 127 LYS cc_start: 0.9484 (mmtp) cc_final: 0.9171 (tppt) REVERT: I 153 ASP cc_start: 0.9018 (t0) cc_final: 0.8576 (p0) REVERT: I 183 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.8441 (t70) REVERT: I 188 MET cc_start: 0.9035 (mmp) cc_final: 0.8461 (mmp) REVERT: I 321 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8316 (p) REVERT: I 337 LYS cc_start: 0.8745 (mmtm) cc_final: 0.8307 (mmmm) REVERT: M 17 GLU cc_start: 0.9578 (tm-30) cc_final: 0.9234 (pt0) REVERT: J 153 ASP cc_start: 0.8948 (t0) cc_final: 0.8519 (p0) REVERT: J 188 MET cc_start: 0.9170 (mtm) cc_final: 0.8538 (mpp) REVERT: J 325 MET cc_start: 0.9194 (ptm) cc_final: 0.8793 (mpp) REVERT: J 337 LYS cc_start: 0.8641 (mttm) cc_final: 0.8041 (mttm) REVERT: K 71 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8413 (p) REVERT: K 153 ASP cc_start: 0.9057 (t0) cc_final: 0.8662 (p0) REVERT: K 325 MET cc_start: 0.8635 (mtp) cc_final: 0.8306 (mtp) REVERT: K 337 LYS cc_start: 0.8710 (mmtm) cc_final: 0.8192 (mmmm) outliers start: 41 outliers final: 35 residues processed: 246 average time/residue: 0.1511 time to fit residues: 51.8545 Evaluate side-chains 242 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 321 THR Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 27 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.074607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046615 restraints weight = 76082.470| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 5.33 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17464 Z= 0.121 Angle : 0.761 17.377 23636 Z= 0.381 Chirality : 0.044 0.211 2677 Planarity : 0.004 0.053 3060 Dihedral : 4.317 56.405 2384 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.87 % Allowed : 20.19 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.41 (0.17), residues: 2180 helix: -0.92 (0.27), residues: 333 sheet: 0.14 (0.20), residues: 714 loop : -1.68 (0.16), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 13 TYR 0.013 0.001 TYR I 264 PHE 0.013 0.001 PHE J 292 TRP 0.016 0.001 TRP B 339 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00281 (17464) covalent geometry : angle 0.76094 (23636) hydrogen bonds : bond 0.03618 ( 476) hydrogen bonds : angle 5.02181 ( 1341) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 MET cc_start: 0.8633 (mpp) cc_final: 0.8374 (mpp) REVERT: B 325 MET cc_start: 0.9241 (mtp) cc_final: 0.8714 (mtp) REVERT: F 111 TYR cc_start: 0.9000 (m-80) cc_final: 0.8594 (m-80) REVERT: F 124 TYR cc_start: 0.9254 (m-80) cc_final: 0.8913 (m-80) REVERT: F 142 HIS cc_start: 0.8835 (OUTLIER) cc_final: 0.7953 (p90) REVERT: F 153 ASP cc_start: 0.9013 (t0) cc_final: 0.8496 (p0) REVERT: F 325 MET cc_start: 0.9284 (mtm) cc_final: 0.8802 (mtp) REVERT: F 337 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8566 (mmmm) REVERT: L 18 GLN cc_start: 0.9061 (tp40) cc_final: 0.8575 (tp40) REVERT: L 21 MET cc_start: 0.8549 (tmm) cc_final: 0.8063 (tmm) REVERT: A 182 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8457 (mm-30) REVERT: H 175 MET cc_start: 0.9543 (mmm) cc_final: 0.9214 (tpp) REVERT: C 182 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8399 (mm-30) REVERT: I 57 LYS cc_start: 0.9305 (mtmm) cc_final: 0.9093 (mmmm) REVERT: I 101 MET cc_start: 0.9209 (ptp) cc_final: 0.8944 (pmm) REVERT: I 127 LYS cc_start: 0.9475 (mmtp) cc_final: 0.9156 (tppt) REVERT: I 153 ASP cc_start: 0.8976 (t0) cc_final: 0.8736 (t0) REVERT: I 183 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.8372 (t70) REVERT: I 188 MET cc_start: 0.9116 (mmp) cc_final: 0.8527 (mmp) REVERT: I 321 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8360 (p) REVERT: I 337 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8313 (mmmm) REVERT: J 153 ASP cc_start: 0.8889 (t0) cc_final: 0.8469 (p0) REVERT: J 188 MET cc_start: 0.9174 (mtm) cc_final: 0.8523 (mpp) REVERT: J 325 MET cc_start: 0.9153 (ptm) cc_final: 0.8642 (ptp) REVERT: J 337 LYS cc_start: 0.8649 (mttm) cc_final: 0.8072 (mttm) REVERT: K 111 TYR cc_start: 0.8927 (m-80) cc_final: 0.8666 (m-80) REVERT: K 142 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.7959 (p90) REVERT: K 153 ASP cc_start: 0.9009 (t0) cc_final: 0.8633 (p0) REVERT: K 325 MET cc_start: 0.8515 (mtp) cc_final: 0.8227 (mtp) REVERT: K 337 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8153 (mmmm) outliers start: 35 outliers final: 28 residues processed: 252 average time/residue: 0.1737 time to fit residues: 61.6411 Evaluate side-chains 244 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 321 THR Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 142 HIS Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 168 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 3 optimal weight: 0.0770 chunk 193 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.074656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.046507 restraints weight = 75594.544| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 5.34 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17464 Z= 0.127 Angle : 0.782 16.828 23636 Z= 0.392 Chirality : 0.044 0.214 2677 Planarity : 0.004 0.053 3060 Dihedral : 4.258 56.914 2384 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.82 % Allowed : 20.94 % Favored : 77.24 % 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: -1.35 (0.17), residues: 2180 helix: -0.94 (0.28), residues: 333 sheet: 0.27 (0.20), residues: 709 loop : -1.68 (0.16), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 13 TYR 0.013 0.001 TYR I 264 PHE 0.013 0.001 PHE K 241 TRP 0.016 0.001 TRP B 339 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00298 (17464) covalent geometry : angle 0.78201 (23636) hydrogen bonds : bond 0.03592 ( 476) hydrogen bonds : angle 4.96035 ( 1341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4082.54 seconds wall clock time: 70 minutes 58.01 seconds (4258.01 seconds total)