Starting phenix.real_space_refine on Sun Jun 15 08:46:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jkb_36367/06_2025/8jkb_36367.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jkb_36367/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jkb_36367/06_2025/8jkb_36367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jkb_36367/06_2025/8jkb_36367.map" model { file = "/net/cci-nas-00/data/ceres_data/8jkb_36367/06_2025/8jkb_36367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jkb_36367/06_2025/8jkb_36367.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.043 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.70, per 1000 atoms: 0.68 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: 4.53 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.48 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: 5.68 Time building geometry restraints manager: 5.38 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 43.280 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (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 TRP 0.023 0.002 TRP K 63 HIS 0.006 0.001 HIS B 311 PHE 0.044 0.002 PHE K 235 TYR 0.035 0.002 TYR I 105 ARG 0.003 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.26094 ( 476) hydrogen bonds : angle 8.06052 ( 1341) covalent geometry : bond 0.00384 (17464) covalent geometry : angle 0.67445 (23636) *********************** 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 : 1.881 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: 0.3810 time to fit residues: 204.9178 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 : 2.195 ------------------------------------------------------------------------------- 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 179 optimal weight: 0.5980 chunk 161 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 101 optimal weight: 0.2980 chunk 124 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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** N 24 ASN N 44 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.078430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.050896 restraints weight = 79005.164| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 5.51 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17464 Z= 0.177 Angle : 0.670 10.170 23636 Z= 0.350 Chirality : 0.044 0.138 2677 Planarity : 0.005 0.136 3060 Dihedral : 4.850 55.740 2384 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.50 % Allowed : 12.00 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.17), residues: 2180 helix: 0.74 (0.29), residues: 309 sheet: -0.72 (0.19), residues: 714 loop : -1.97 (0.16), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 179 HIS 0.005 0.001 HIS H 156 PHE 0.015 0.002 PHE G 61 TYR 0.025 0.001 TYR J 111 ARG 0.005 0.000 ARG I 19 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 476) hydrogen bonds : angle 5.44395 ( 1341) covalent geometry : bond 0.00398 (17464) covalent geometry : angle 0.66980 (23636) *********************** 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 299 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 2.146 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: B 153 ASP cc_start: 0.8759 (t0) cc_final: 0.8331 (p0) REVERT: B 325 MET cc_start: 0.9280 (mtp) cc_final: 0.8758 (mtp) REVERT: G 9 ILE cc_start: 0.5767 (tp) cc_final: 0.5508 (pt) REVERT: F 124 TYR cc_start: 0.9329 (m-80) cc_final: 0.8999 (m-80) REVERT: F 127 LYS cc_start: 0.9384 (tppt) cc_final: 0.9124 (tppt) REVERT: F 217 MET cc_start: 0.8945 (mmm) cc_final: 0.8722 (mmm) REVERT: F 325 MET cc_start: 0.9419 (mtm) cc_final: 0.8924 (mtp) REVERT: F 339 TRP cc_start: 0.8818 (m100) cc_final: 0.7667 (m100) REVERT: L 21 MET cc_start: 0.9007 (tmm) cc_final: 0.8619 (ppp) REVERT: D 180 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8698 (mmmt) REVERT: E 165 GLU cc_start: 0.9007 (pp20) cc_final: 0.8713 (pm20) REVERT: E 182 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8235 (mm-30) REVERT: I 57 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8888 (mtpp) REVERT: I 127 LYS cc_start: 0.9542 (mmtp) cc_final: 0.9231 (tppt) REVERT: I 153 ASP cc_start: 0.8939 (t0) cc_final: 0.8529 (p0) REVERT: I 337 LYS cc_start: 0.8647 (mmtm) cc_final: 0.8311 (mmmm) REVERT: M 21 MET cc_start: 0.9108 (tmm) cc_final: 0.8880 (ppp) REVERT: M 32 LYS cc_start: 0.9821 (pttt) cc_final: 0.9463 (pttp) REVERT: J 153 ASP cc_start: 0.8825 (t0) cc_final: 0.8398 (p0) REVERT: J 188 MET cc_start: 0.9161 (mtm) cc_final: 0.8794 (mtm) REVERT: J 262 MET cc_start: 0.8382 (mpp) cc_final: 0.8064 (mpp) REVERT: J 311 HIS cc_start: 0.8452 (m-70) cc_final: 0.7575 (m-70) REVERT: J 325 MET cc_start: 0.9150 (ptm) cc_final: 0.8901 (ptp) REVERT: J 337 LYS cc_start: 0.8564 (mttm) cc_final: 0.8128 (ptpt) REVERT: K 127 LYS cc_start: 0.9536 (mmtp) cc_final: 0.9303 (tppt) REVERT: K 153 ASP cc_start: 0.8821 (t0) cc_final: 0.8492 (p0) REVERT: K 325 MET cc_start: 0.8867 (mtp) cc_final: 0.8486 (mtp) REVERT: K 337 LYS cc_start: 0.8662 (mmtm) cc_final: 0.8187 (mmmm) outliers start: 28 outliers final: 15 residues processed: 283 average time/residue: 0.3960 time to fit residues: 153.8926 Evaluate side-chains 242 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 227 time to evaluate : 2.021 ------------------------------------------------------------------------------- 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 187 ILE Chi-restraints excluded: chain I residue 12 GLU 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 120 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 140 optimal weight: 40.0000 chunk 99 optimal weight: 40.0000 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 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 G 18 GLN ** 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** ** I 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.075721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047275 restraints weight = 74602.871| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 5.34 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17464 Z= 0.196 Angle : 0.638 11.800 23636 Z= 0.333 Chirality : 0.043 0.139 2677 Planarity : 0.005 0.094 3060 Dihedral : 4.716 55.239 2384 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.14 % Allowed : 13.12 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.17), residues: 2180 helix: 0.40 (0.28), residues: 311 sheet: -0.61 (0.20), residues: 716 loop : -1.91 (0.16), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 179 HIS 0.012 0.001 HIS F 142 PHE 0.017 0.001 PHE K 241 TYR 0.019 0.001 TYR J 145 ARG 0.004 0.000 ARG F 42 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 476) hydrogen bonds : angle 5.16495 ( 1341) covalent geometry : bond 0.00441 (17464) covalent geometry : angle 0.63820 (23636) *********************** 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 275 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 2.020 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: B 153 ASP cc_start: 0.8938 (t0) cc_final: 0.8525 (p0) REVERT: F 61 MET cc_start: 0.8766 (ppp) cc_final: 0.8508 (ppp) REVERT: F 111 TYR cc_start: 0.8919 (m-80) cc_final: 0.8425 (m-80) REVERT: F 127 LYS cc_start: 0.9419 (tppt) cc_final: 0.9206 (tppt) REVERT: F 325 MET cc_start: 0.9405 (mtm) cc_final: 0.8901 (mtp) REVERT: F 339 TRP cc_start: 0.8979 (m100) cc_final: 0.8301 (m100) REVERT: L 21 MET cc_start: 0.8914 (tmm) cc_final: 0.8631 (tmm) REVERT: H 167 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: E 180 LYS cc_start: 0.9413 (mtpp) cc_final: 0.9152 (mtpp) REVERT: E 182 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8121 (mm-30) REVERT: I 57 LYS cc_start: 0.9260 (mtmm) cc_final: 0.8930 (mtpp) REVERT: I 127 LYS cc_start: 0.9528 (mmtp) cc_final: 0.9210 (tppt) REVERT: I 145 TYR cc_start: 0.9261 (p90) cc_final: 0.9035 (p90) REVERT: I 153 ASP cc_start: 0.8884 (t0) cc_final: 0.8439 (p0) REVERT: I 337 LYS cc_start: 0.8718 (mmtm) cc_final: 0.8316 (mmmm) REVERT: M 21 MET cc_start: 0.9039 (tmm) cc_final: 0.8784 (ppp) REVERT: J 12 GLU cc_start: 0.9720 (pp20) cc_final: 0.9506 (pp20) REVERT: J 153 ASP cc_start: 0.8843 (t0) cc_final: 0.8434 (p0) REVERT: J 188 MET cc_start: 0.9156 (mtm) cc_final: 0.8730 (mtm) REVERT: J 292 PHE cc_start: 0.9326 (m-80) cc_final: 0.9050 (m-80) REVERT: J 311 HIS cc_start: 0.8701 (m-70) cc_final: 0.7313 (m-70) REVERT: J 325 MET cc_start: 0.9278 (ptm) cc_final: 0.8935 (ptp) REVERT: J 337 LYS cc_start: 0.8540 (mttm) cc_final: 0.8080 (ptpt) REVERT: K 127 LYS cc_start: 0.9537 (mmtp) cc_final: 0.9290 (tppt) REVERT: K 153 ASP cc_start: 0.8963 (t0) cc_final: 0.8593 (p0) REVERT: K 325 MET cc_start: 0.8859 (mtp) cc_final: 0.8504 (mtp) REVERT: K 337 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8235 (mmmm) outliers start: 40 outliers final: 26 residues processed: 254 average time/residue: 0.3806 time to fit residues: 134.3343 Evaluate side-chains 232 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain F residue 10 GLU 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 A residue 168 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 209 LEU 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 J residue 142 HIS Chi-restraints excluded: chain J residue 223 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 190 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN I 311 HIS ** I 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.074950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.046792 restraints weight = 75834.031| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 5.30 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17464 Z= 0.179 Angle : 0.622 13.254 23636 Z= 0.322 Chirality : 0.043 0.144 2677 Planarity : 0.004 0.063 3060 Dihedral : 4.610 55.073 2384 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.57 % Allowed : 14.68 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2180 helix: 0.13 (0.27), residues: 329 sheet: -0.47 (0.20), residues: 714 loop : -1.85 (0.16), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 339 HIS 0.005 0.001 HIS C 156 PHE 0.016 0.001 PHE K 241 TYR 0.014 0.001 TYR J 111 ARG 0.006 0.000 ARG J 8 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 476) hydrogen bonds : angle 5.06781 ( 1341) covalent geometry : bond 0.00403 (17464) covalent geometry : angle 0.62197 (23636) *********************** 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 281 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 233 time to evaluate : 2.058 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: 0.9763 (pp20) cc_final: 0.9490 (pp20) REVERT: B 153 ASP cc_start: 0.8969 (t0) cc_final: 0.8550 (p0) REVERT: B 325 MET cc_start: 0.9181 (mtp) cc_final: 0.8734 (mmm) REVERT: F 12 GLU cc_start: 0.9732 (pp20) cc_final: 0.9453 (pp20) REVERT: F 111 TYR cc_start: 0.8913 (m-80) cc_final: 0.8512 (m-80) REVERT: F 142 HIS cc_start: 0.8620 (p-80) cc_final: 0.8310 (p90) REVERT: F 153 ASP cc_start: 0.8925 (t0) cc_final: 0.8432 (p0) REVERT: F 325 MET cc_start: 0.9381 (mtm) cc_final: 0.8886 (mtp) REVERT: F 339 TRP cc_start: 0.9031 (m100) cc_final: 0.8506 (m100) REVERT: L 21 MET cc_start: 0.8675 (tmm) cc_final: 0.8301 (tmm) REVERT: H 165 GLU cc_start: 0.9313 (tm-30) cc_final: 0.9059 (pt0) REVERT: H 167 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: D 175 MET cc_start: 0.9355 (tpp) cc_final: 0.8830 (tpp) REVERT: E 180 LYS cc_start: 0.9463 (mtpp) cc_final: 0.9173 (mtpp) REVERT: E 182 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8080 (mm-30) REVERT: I 57 LYS cc_start: 0.9298 (mtmm) cc_final: 0.9003 (mtpp) REVERT: I 127 LYS cc_start: 0.9532 (mmtp) cc_final: 0.9206 (tppt) REVERT: I 153 ASP cc_start: 0.8882 (t0) cc_final: 0.8484 (p0) REVERT: I 183 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8322 (t70) REVERT: I 337 LYS cc_start: 0.8763 (mmtm) cc_final: 0.8352 (mmmm) REVERT: M 21 MET cc_start: 0.9063 (tmm) cc_final: 0.8806 (ppp) REVERT: J 12 GLU cc_start: 0.9629 (pp20) cc_final: 0.9272 (pp20) REVERT: J 153 ASP cc_start: 0.8895 (t0) cc_final: 0.8489 (p0) REVERT: J 188 MET cc_start: 0.9143 (mtm) cc_final: 0.8528 (mpp) REVERT: J 292 PHE cc_start: 0.9370 (m-80) cc_final: 0.8843 (m-80) REVERT: J 325 MET cc_start: 0.9251 (ptm) cc_final: 0.8877 (ptp) REVERT: J 337 LYS cc_start: 0.8608 (mttm) cc_final: 0.8002 (mttm) REVERT: K 127 LYS cc_start: 0.9515 (mmtp) cc_final: 0.9252 (tppt) REVERT: K 153 ASP cc_start: 0.9020 (t0) cc_final: 0.8640 (p0) REVERT: K 325 MET cc_start: 0.8764 (mtp) cc_final: 0.8304 (mtp) REVERT: K 337 LYS cc_start: 0.8747 (mmtm) cc_final: 0.8228 (mmmm) outliers start: 48 outliers final: 28 residues processed: 261 average time/residue: 0.3805 time to fit residues: 139.2114 Evaluate side-chains 238 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 338 ILE 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 166 GLU 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 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 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 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 157 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 115 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 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 = 0.3677 r_free = 0.3677 target = 0.074459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.046436 restraints weight = 75977.207| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 5.31 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17464 Z= 0.166 Angle : 0.624 9.486 23636 Z= 0.322 Chirality : 0.043 0.143 2677 Planarity : 0.004 0.059 3060 Dihedral : 4.482 54.479 2384 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.25 % Allowed : 16.39 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2180 helix: 0.02 (0.28), residues: 323 sheet: -0.35 (0.20), residues: 716 loop : -1.82 (0.16), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 297 HIS 0.005 0.001 HIS C 156 PHE 0.015 0.001 PHE K 241 TYR 0.019 0.001 TYR J 145 ARG 0.004 0.000 ARG J 8 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 476) hydrogen bonds : angle 4.96577 ( 1341) covalent geometry : bond 0.00374 (17464) covalent geometry : angle 0.62367 (23636) *********************** 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 275 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 1.967 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: B 153 ASP cc_start: 0.8966 (t0) cc_final: 0.8536 (p0) REVERT: B 325 MET cc_start: 0.9197 (mtp) cc_final: 0.8715 (mmm) REVERT: F 111 TYR cc_start: 0.8946 (m-80) cc_final: 0.8586 (m-80) REVERT: F 142 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.8280 (p90) REVERT: F 153 ASP cc_start: 0.8940 (t0) cc_final: 0.8477 (p0) REVERT: F 325 MET cc_start: 0.9365 (mtm) cc_final: 0.8829 (mtp) REVERT: L 21 MET cc_start: 0.8591 (tmm) cc_final: 0.8216 (tmm) REVERT: A 165 GLU cc_start: 0.8419 (pm20) cc_final: 0.8055 (pm20) REVERT: H 165 GLU cc_start: 0.9338 (tm-30) cc_final: 0.9132 (pt0) REVERT: H 166 GLU cc_start: 0.8591 (mp0) cc_final: 0.8186 (mp0) REVERT: H 167 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: H 182 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8445 (mm-30) REVERT: D 175 MET cc_start: 0.9410 (tpp) cc_final: 0.9025 (tpp) REVERT: D 182 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8495 (mm-30) REVERT: E 180 LYS cc_start: 0.9493 (mtpp) cc_final: 0.9200 (mtpp) REVERT: E 182 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8061 (mm-30) REVERT: I 12 GLU cc_start: 0.9753 (pp20) cc_final: 0.9520 (pp20) REVERT: I 57 LYS cc_start: 0.9310 (mtmm) cc_final: 0.9015 (mtpp) REVERT: I 101 MET cc_start: 0.9119 (ptp) cc_final: 0.8825 (pmm) REVERT: I 127 LYS cc_start: 0.9518 (mmtp) cc_final: 0.9194 (tppt) REVERT: I 153 ASP cc_start: 0.8891 (t0) cc_final: 0.8471 (p0) REVERT: I 183 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8355 (t70) REVERT: I 217 MET cc_start: 0.8901 (mmm) cc_final: 0.8697 (mmm) REVERT: I 337 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8322 (mmmm) REVERT: M 17 GLU cc_start: 0.9564 (tm-30) cc_final: 0.9161 (pt0) REVERT: M 21 MET cc_start: 0.9048 (tmm) cc_final: 0.8814 (ppp) REVERT: J 153 ASP cc_start: 0.8924 (t0) cc_final: 0.8511 (p0) REVERT: J 188 MET cc_start: 0.9142 (mtm) cc_final: 0.8509 (mpp) REVERT: J 325 MET cc_start: 0.9210 (ptm) cc_final: 0.8848 (ptp) REVERT: J 337 LYS cc_start: 0.8648 (mttm) cc_final: 0.8128 (mttm) REVERT: K 57 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8449 (mmmm) REVERT: K 78 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7942 (ttpt) REVERT: K 127 LYS cc_start: 0.9513 (mmtp) cc_final: 0.9250 (tppt) REVERT: K 153 ASP cc_start: 0.9040 (t0) cc_final: 0.8659 (p0) REVERT: K 188 MET cc_start: 0.8815 (mmm) cc_final: 0.8548 (mmp) REVERT: K 325 MET cc_start: 0.8647 (mtp) cc_final: 0.8285 (mtp) REVERT: K 337 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8274 (mmmm) outliers start: 42 outliers final: 29 residues processed: 258 average time/residue: 0.3680 time to fit residues: 133.1750 Evaluate side-chains 234 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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 142 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 338 ILE 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 166 GLU 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 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 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 J residue 339 TRP Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 78 LYS Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 157 ILE 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 171 optimal weight: 8.9990 chunk 158 optimal weight: 0.0040 chunk 163 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 chunk 61 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 overall best weight: 3.2198 ------------------------------------------------------------------------------- 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** F 259 GLN ** I 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN ** N 18 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 = 0.3660 r_free = 0.3660 target = 0.073607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.045353 restraints weight = 77053.066| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 5.36 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17464 Z= 0.193 Angle : 0.657 13.723 23636 Z= 0.337 Chirality : 0.043 0.143 2677 Planarity : 0.004 0.054 3060 Dihedral : 4.556 55.305 2384 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.00 % Allowed : 16.34 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.17), residues: 2180 helix: -0.34 (0.27), residues: 322 sheet: -0.34 (0.19), residues: 741 loop : -1.81 (0.16), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 339 HIS 0.005 0.001 HIS C 156 PHE 0.014 0.001 PHE K 241 TYR 0.033 0.001 TYR K 145 ARG 0.010 0.000 ARG J 8 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 476) hydrogen bonds : angle 5.05790 ( 1341) covalent geometry : bond 0.00434 (17464) covalent geometry : angle 0.65718 (23636) *********************** 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 285 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 1.903 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 12 GLU cc_start: 0.9708 (pp20) cc_final: 0.9438 (pp20) REVERT: B 153 ASP cc_start: 0.9001 (t0) cc_final: 0.8576 (p0) REVERT: B 325 MET cc_start: 0.9252 (mtp) cc_final: 0.8278 (ttt) REVERT: F 12 GLU cc_start: 0.9714 (pp20) cc_final: 0.9418 (pp20) REVERT: F 61 MET cc_start: 0.8719 (ppp) cc_final: 0.8410 (ppp) REVERT: F 111 TYR cc_start: 0.8999 (m-80) cc_final: 0.8549 (m-80) REVERT: F 142 HIS cc_start: 0.8886 (OUTLIER) cc_final: 0.8263 (p-80) REVERT: F 153 ASP cc_start: 0.8999 (t0) cc_final: 0.8481 (p0) REVERT: F 217 MET cc_start: 0.8927 (mmm) cc_final: 0.8724 (mmm) REVERT: F 325 MET cc_start: 0.9307 (mtm) cc_final: 0.8767 (mtp) REVERT: L 21 MET cc_start: 0.8558 (tmm) cc_final: 0.8131 (tmm) REVERT: A 167 GLU cc_start: 0.8724 (pm20) cc_final: 0.8393 (pm20) REVERT: A 182 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8473 (mm-30) REVERT: H 165 GLU cc_start: 0.9346 (tm-30) cc_final: 0.9065 (pt0) REVERT: H 166 GLU cc_start: 0.8464 (mp0) cc_final: 0.8014 (mp0) REVERT: H 167 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: H 182 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8413 (mm-30) REVERT: D 175 MET cc_start: 0.9496 (tpp) cc_final: 0.9013 (tpp) REVERT: E 175 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.9209 (mmm) REVERT: E 180 LYS cc_start: 0.9512 (mtpp) cc_final: 0.9219 (mtpp) REVERT: E 182 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8066 (mm-30) REVERT: I 57 LYS cc_start: 0.9322 (mtmm) cc_final: 0.9018 (mtpp) REVERT: I 127 LYS cc_start: 0.9512 (mmtp) cc_final: 0.9198 (tppt) REVERT: I 153 ASP cc_start: 0.8905 (t0) cc_final: 0.8517 (p0) REVERT: I 183 HIS cc_start: 0.8748 (OUTLIER) cc_final: 0.8402 (t70) REVERT: I 188 MET cc_start: 0.9025 (mmp) cc_final: 0.8533 (mmp) REVERT: I 264 TYR cc_start: 0.9104 (m-10) cc_final: 0.8879 (m-80) REVERT: I 337 LYS cc_start: 0.8797 (mmtm) cc_final: 0.8362 (mmmm) REVERT: M 21 MET cc_start: 0.9039 (tmm) cc_final: 0.8780 (ppp) REVERT: J 12 GLU cc_start: 0.9715 (pp20) cc_final: 0.9496 (pp20) REVERT: J 153 ASP cc_start: 0.8923 (t0) cc_final: 0.8576 (p0) REVERT: J 188 MET cc_start: 0.9165 (mtm) cc_final: 0.8525 (mpp) REVERT: J 292 PHE cc_start: 0.9399 (m-80) cc_final: 0.8921 (m-10) REVERT: J 325 MET cc_start: 0.9222 (ptm) cc_final: 0.8725 (ptp) REVERT: J 337 LYS cc_start: 0.8664 (mttm) cc_final: 0.8108 (mttm) REVERT: K 57 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8507 (mmmm) REVERT: K 61 MET cc_start: 0.8605 (ppp) cc_final: 0.8080 (ppp) REVERT: K 78 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7993 (ttpt) REVERT: K 127 LYS cc_start: 0.9502 (mmtp) cc_final: 0.9247 (tppt) REVERT: K 153 ASP cc_start: 0.9053 (t0) cc_final: 0.8647 (p0) REVERT: K 188 MET cc_start: 0.9014 (mmm) cc_final: 0.8709 (mmp) REVERT: K 325 MET cc_start: 0.8686 (mtp) cc_final: 0.8333 (mtp) REVERT: K 337 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8285 (mmmm) outliers start: 56 outliers final: 39 residues processed: 266 average time/residue: 0.3642 time to fit residues: 135.3845 Evaluate side-chains 252 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 1.985 ------------------------------------------------------------------------------- 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 312 ASP Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER 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 338 ILE 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 166 GLU 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 168 LEU 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 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 142 HIS 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 57 LYS Chi-restraints excluded: chain K residue 78 LYS Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 296 VAL 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 45 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 60 optimal weight: 0.2980 chunk 16 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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** I 88 ASN ** I 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.074412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.046295 restraints weight = 76002.571| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 5.33 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17464 Z= 0.126 Angle : 0.653 11.986 23636 Z= 0.333 Chirality : 0.043 0.141 2677 Planarity : 0.004 0.054 3060 Dihedral : 4.350 55.231 2384 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.57 % Allowed : 17.78 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.17), residues: 2180 helix: -0.57 (0.27), residues: 322 sheet: -0.20 (0.19), residues: 741 loop : -1.74 (0.16), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS G 44 PHE 0.014 0.001 PHE K 241 TYR 0.029 0.001 TYR B 145 ARG 0.008 0.000 ARG J 8 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 476) hydrogen bonds : angle 4.93838 ( 1341) covalent geometry : bond 0.00288 (17464) covalent geometry : angle 0.65318 (23636) *********************** 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 277 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 1.946 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 153 ASP cc_start: 0.8977 (t0) cc_final: 0.8549 (p0) REVERT: B 325 MET cc_start: 0.9221 (mtp) cc_final: 0.8226 (ttt) REVERT: F 61 MET cc_start: 0.8703 (ppp) cc_final: 0.8340 (ppp) REVERT: F 111 TYR cc_start: 0.8983 (m-80) cc_final: 0.8595 (m-80) REVERT: F 142 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8129 (p-80) REVERT: F 153 ASP cc_start: 0.8990 (t0) cc_final: 0.8471 (p0) REVERT: F 325 MET cc_start: 0.9299 (mtm) cc_final: 0.8787 (mtp) REVERT: L 21 MET cc_start: 0.8569 (tmm) cc_final: 0.8141 (tmm) REVERT: A 165 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: A 167 GLU cc_start: 0.8736 (pm20) cc_final: 0.8408 (pm20) REVERT: H 165 GLU cc_start: 0.9316 (tm-30) cc_final: 0.9017 (pt0) REVERT: H 166 GLU cc_start: 0.8467 (mp0) cc_final: 0.8098 (mp0) REVERT: H 167 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7979 (pm20) REVERT: H 175 MET cc_start: 0.9469 (tpp) cc_final: 0.8587 (mpp) REVERT: H 182 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8429 (mm-30) REVERT: C 182 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8374 (mm-30) REVERT: D 175 MET cc_start: 0.9529 (tpp) cc_final: 0.8986 (tpp) REVERT: E 182 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8089 (mm-30) REVERT: I 57 LYS cc_start: 0.9310 (mtmm) cc_final: 0.9028 (mtpp) REVERT: I 101 MET cc_start: 0.9154 (ptp) cc_final: 0.8871 (pmm) REVERT: I 127 LYS cc_start: 0.9502 (mmtp) cc_final: 0.9183 (tppt) REVERT: I 153 ASP cc_start: 0.8906 (t0) cc_final: 0.8699 (t0) REVERT: I 183 HIS cc_start: 0.8708 (OUTLIER) cc_final: 0.8394 (t70) REVERT: I 264 TYR cc_start: 0.9035 (m-10) cc_final: 0.8801 (m-80) REVERT: I 337 LYS cc_start: 0.8779 (mmtm) cc_final: 0.8340 (mmmm) REVERT: M 17 GLU cc_start: 0.9551 (tm-30) cc_final: 0.9235 (pt0) REVERT: M 21 MET cc_start: 0.9038 (tmm) cc_final: 0.8808 (ppp) REVERT: J 153 ASP cc_start: 0.8967 (t0) cc_final: 0.8551 (p0) REVERT: J 188 MET cc_start: 0.9126 (mtm) cc_final: 0.8501 (mpp) REVERT: J 292 PHE cc_start: 0.9420 (m-80) cc_final: 0.8933 (m-10) REVERT: J 325 MET cc_start: 0.9193 (ptm) cc_final: 0.8809 (mpp) REVERT: J 337 LYS cc_start: 0.8620 (mttm) cc_final: 0.8096 (mttm) REVERT: K 61 MET cc_start: 0.8580 (ppp) cc_final: 0.8125 (ppp) REVERT: K 71 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8345 (p) REVERT: K 127 LYS cc_start: 0.9505 (mmtp) cc_final: 0.9246 (tppt) REVERT: K 153 ASP cc_start: 0.9040 (t0) cc_final: 0.8657 (p0) REVERT: K 188 MET cc_start: 0.8988 (mmm) cc_final: 0.8716 (mmp) REVERT: K 325 MET cc_start: 0.8622 (mtp) cc_final: 0.8298 (mtp) REVERT: K 337 LYS cc_start: 0.8738 (mmtm) cc_final: 0.8228 (mmmm) outliers start: 48 outliers final: 36 residues processed: 264 average time/residue: 0.3560 time to fit residues: 131.9912 Evaluate side-chains 249 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 2.092 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER 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 F residue 338 ILE 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 165 GLU Chi-restraints excluded: chain A residue 166 GLU 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 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 M residue 13 ARG Chi-restraints excluded: chain M residue 24 ASN 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 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 134 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** ** I 340 ASN ** 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 = 0.3671 r_free = 0.3671 target = 0.074015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045748 restraints weight = 76199.848| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 5.35 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17464 Z= 0.147 Angle : 0.684 15.914 23636 Z= 0.345 Chirality : 0.043 0.138 2677 Planarity : 0.004 0.055 3060 Dihedral : 4.338 55.667 2384 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.46 % Allowed : 18.53 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.17), residues: 2180 helix: -0.56 (0.28), residues: 322 sheet: -0.05 (0.20), residues: 716 loop : -1.75 (0.16), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.004 0.001 HIS C 156 PHE 0.014 0.001 PHE K 241 TYR 0.008 0.001 TYR F 105 ARG 0.009 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 476) hydrogen bonds : angle 4.94349 ( 1341) covalent geometry : bond 0.00336 (17464) covalent geometry : angle 0.68389 (23636) *********************** 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 276 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 1.955 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 153 ASP cc_start: 0.9020 (t0) cc_final: 0.8592 (p0) REVERT: B 325 MET cc_start: 0.9261 (mtp) cc_final: 0.8302 (ttt) REVERT: F 61 MET cc_start: 0.8609 (ppp) cc_final: 0.8375 (ppp) REVERT: F 111 TYR cc_start: 0.8983 (m-80) cc_final: 0.8568 (m-80) REVERT: F 142 HIS cc_start: 0.8953 (OUTLIER) cc_final: 0.8176 (p-80) REVERT: F 153 ASP cc_start: 0.8991 (t0) cc_final: 0.8486 (p0) REVERT: F 325 MET cc_start: 0.9337 (mtm) cc_final: 0.8815 (mtp) REVERT: L 21 MET cc_start: 0.8508 (tmm) cc_final: 0.8108 (tmm) REVERT: A 167 GLU cc_start: 0.8809 (pm20) cc_final: 0.8453 (pm20) REVERT: H 165 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9030 (pt0) REVERT: H 166 GLU cc_start: 0.8442 (mp0) cc_final: 0.8159 (mp0) REVERT: H 167 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: C 182 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8387 (mm-30) REVERT: D 175 MET cc_start: 0.9568 (tpp) cc_final: 0.9251 (tpp) REVERT: D 182 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8466 (mm-30) REVERT: E 182 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8119 (mm-30) REVERT: I 57 LYS cc_start: 0.9320 (mtmm) cc_final: 0.9027 (mtpp) REVERT: I 101 MET cc_start: 0.9134 (ptp) cc_final: 0.8834 (pmm) REVERT: I 127 LYS cc_start: 0.9498 (mmtp) cc_final: 0.9169 (tppt) REVERT: I 183 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.8356 (t70) REVERT: I 264 TYR cc_start: 0.8996 (m-80) cc_final: 0.8758 (m-80) REVERT: I 337 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8314 (mmmm) REVERT: M 17 GLU cc_start: 0.9552 (tm-30) cc_final: 0.9137 (pt0) REVERT: M 21 MET cc_start: 0.9020 (tmm) cc_final: 0.8809 (ppp) REVERT: J 153 ASP cc_start: 0.8953 (t0) cc_final: 0.8535 (p0) REVERT: J 188 MET cc_start: 0.9145 (mtm) cc_final: 0.8513 (mpp) REVERT: J 292 PHE cc_start: 0.9429 (m-80) cc_final: 0.8925 (m-10) REVERT: J 325 MET cc_start: 0.9182 (ptm) cc_final: 0.8808 (mpp) REVERT: J 337 LYS cc_start: 0.8638 (mttm) cc_final: 0.8108 (mttm) REVERT: K 61 MET cc_start: 0.8572 (ppp) cc_final: 0.8130 (ppp) REVERT: K 71 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8310 (m) REVERT: K 153 ASP cc_start: 0.9059 (t0) cc_final: 0.8744 (p0) REVERT: K 188 MET cc_start: 0.9038 (mmm) cc_final: 0.8775 (mmp) REVERT: K 325 MET cc_start: 0.8648 (mtp) cc_final: 0.8328 (mtp) REVERT: K 337 LYS cc_start: 0.8707 (mmtm) cc_final: 0.8191 (mmmm) outliers start: 46 outliers final: 36 residues processed: 261 average time/residue: 0.3700 time to fit residues: 136.2842 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 : 2.067 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER 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 292 PHE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain A residue 166 GLU 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 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 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 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 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 171 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 97 optimal weight: 0.0670 chunk 158 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- 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** ** I 340 ASN ** 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 = 0.3682 r_free = 0.3682 target = 0.074427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045993 restraints weight = 76570.400| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 5.38 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17464 Z= 0.129 Angle : 0.712 15.228 23636 Z= 0.358 Chirality : 0.043 0.172 2677 Planarity : 0.004 0.071 3060 Dihedral : 4.254 55.586 2384 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.09 % Allowed : 19.44 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.17), residues: 2180 helix: -0.68 (0.28), residues: 326 sheet: 0.05 (0.20), residues: 712 loop : -1.70 (0.16), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.003 0.001 HIS M 44 PHE 0.013 0.001 PHE K 241 TYR 0.008 0.001 TYR F 264 ARG 0.014 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 476) hydrogen bonds : angle 4.92353 ( 1341) covalent geometry : bond 0.00299 (17464) covalent geometry : angle 0.71169 (23636) *********************** 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 269 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 2.008 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: B 325 MET cc_start: 0.9234 (mtp) cc_final: 0.8694 (mtp) REVERT: F 111 TYR cc_start: 0.9006 (m-80) cc_final: 0.8607 (m-80) REVERT: F 124 TYR cc_start: 0.9223 (m-80) cc_final: 0.8887 (m-80) REVERT: F 142 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.8131 (p-80) REVERT: F 153 ASP cc_start: 0.9021 (t0) cc_final: 0.8531 (p0) REVERT: F 325 MET cc_start: 0.9309 (mtm) cc_final: 0.8787 (mtp) REVERT: L 21 MET cc_start: 0.8503 (tmm) cc_final: 0.8088 (tmm) REVERT: A 165 GLU cc_start: 0.8412 (pm20) cc_final: 0.7740 (pm20) REVERT: A 167 GLU cc_start: 0.8868 (pm20) cc_final: 0.8440 (pm20) REVERT: A 182 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8466 (mm-30) REVERT: H 165 GLU cc_start: 0.9274 (tm-30) cc_final: 0.9010 (pt0) REVERT: H 166 GLU cc_start: 0.8405 (mp0) cc_final: 0.8155 (mp0) REVERT: H 167 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: C 182 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8404 (mm-30) REVERT: D 175 MET cc_start: 0.9572 (tpp) cc_final: 0.9309 (tpp) REVERT: E 180 LYS cc_start: 0.9510 (mtpp) cc_final: 0.9251 (mtpp) REVERT: I 57 LYS cc_start: 0.9330 (mtmm) cc_final: 0.9078 (mtpp) REVERT: I 101 MET cc_start: 0.9162 (ptp) cc_final: 0.8880 (pmm) REVERT: I 127 LYS cc_start: 0.9494 (mmtp) cc_final: 0.9162 (tppt) REVERT: I 183 HIS cc_start: 0.8724 (OUTLIER) cc_final: 0.8370 (t70) REVERT: I 188 MET cc_start: 0.9101 (mmp) cc_final: 0.8538 (mmp) REVERT: I 264 TYR cc_start: 0.8957 (m-80) cc_final: 0.8706 (m-80) REVERT: I 337 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8315 (mmmm) REVERT: M 17 GLU cc_start: 0.9542 (tm-30) cc_final: 0.9218 (pt0) REVERT: M 21 MET cc_start: 0.9045 (tmm) cc_final: 0.8826 (ppp) REVERT: J 153 ASP cc_start: 0.8938 (t0) cc_final: 0.8517 (p0) REVERT: J 188 MET cc_start: 0.9138 (mtm) cc_final: 0.8501 (mpp) REVERT: J 292 PHE cc_start: 0.9453 (m-80) cc_final: 0.8954 (m-10) REVERT: J 325 MET cc_start: 0.9098 (ptm) cc_final: 0.8768 (mpp) REVERT: J 337 LYS cc_start: 0.8604 (mttm) cc_final: 0.8075 (mttm) REVERT: K 61 MET cc_start: 0.8553 (ppp) cc_final: 0.8091 (ppp) REVERT: K 71 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8349 (p) REVERT: K 153 ASP cc_start: 0.9009 (t0) cc_final: 0.8663 (p0) REVERT: K 188 MET cc_start: 0.9053 (mmm) cc_final: 0.8813 (mmp) REVERT: K 325 MET cc_start: 0.8548 (mtp) cc_final: 0.8265 (mtp) REVERT: K 337 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8140 (mmmm) outliers start: 39 outliers final: 32 residues processed: 257 average time/residue: 0.3687 time to fit residues: 132.9071 Evaluate side-chains 250 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 2.076 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER 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 F residue 338 ILE 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 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 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 294 CYS Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain O residue 24 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 74 optimal weight: 0.0980 chunk 56 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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** ** I 340 ASN ** 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 = 0.3669 r_free = 0.3669 target = 0.073456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.045211 restraints weight = 76876.653| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 5.34 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17464 Z= 0.181 Angle : 0.755 14.573 23636 Z= 0.384 Chirality : 0.044 0.207 2677 Planarity : 0.004 0.057 3060 Dihedral : 4.408 56.548 2384 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.98 % Allowed : 19.76 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.17), residues: 2180 helix: -0.77 (0.29), residues: 326 sheet: -0.12 (0.19), residues: 747 loop : -1.65 (0.16), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 339 HIS 0.005 0.001 HIS C 156 PHE 0.013 0.001 PHE K 241 TYR 0.009 0.001 TYR F 105 ARG 0.015 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 476) hydrogen bonds : angle 5.09736 ( 1341) covalent geometry : bond 0.00414 (17464) covalent geometry : angle 0.75545 (23636) ********************** 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 260 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 1.988 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 325 MET cc_start: 0.9272 (mtp) cc_final: 0.8343 (ttt) REVERT: G 47 GLU cc_start: 0.9218 (mp0) cc_final: 0.8942 (pm20) REVERT: F 111 TYR cc_start: 0.8989 (m-80) cc_final: 0.8545 (m-80) REVERT: F 142 HIS cc_start: 0.8991 (OUTLIER) cc_final: 0.8133 (p-80) REVERT: F 153 ASP cc_start: 0.9015 (t0) cc_final: 0.8508 (p0) REVERT: F 325 MET cc_start: 0.9342 (mtm) cc_final: 0.8818 (mtp) REVERT: F 337 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8498 (mmmm) REVERT: L 18 GLN cc_start: 0.9106 (tp-100) cc_final: 0.8807 (tp40) REVERT: L 21 MET cc_start: 0.8585 (tmm) cc_final: 0.8187 (tmm) REVERT: A 167 GLU cc_start: 0.8984 (pm20) cc_final: 0.8608 (pm20) REVERT: A 182 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8482 (mm-30) REVERT: H 165 GLU cc_start: 0.9291 (tm-30) cc_final: 0.9033 (pt0) REVERT: H 175 MET cc_start: 0.9580 (mmm) cc_final: 0.9349 (tpp) REVERT: C 182 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8382 (mm-30) REVERT: D 175 MET cc_start: 0.9601 (tpp) cc_final: 0.9323 (tpp) REVERT: D 182 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8551 (mm-30) REVERT: E 180 LYS cc_start: 0.9529 (mtpp) cc_final: 0.9296 (mtpp) REVERT: E 182 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8172 (mm-30) REVERT: I 57 LYS cc_start: 0.9338 (mtmm) cc_final: 0.9016 (mtpp) REVERT: I 127 LYS cc_start: 0.9488 (mmtp) cc_final: 0.9160 (tppt) REVERT: I 183 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8370 (t70) REVERT: I 188 MET cc_start: 0.9102 (mmp) cc_final: 0.8508 (mmp) REVERT: I 264 TYR cc_start: 0.8943 (m-80) cc_final: 0.8704 (m-80) REVERT: I 337 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8310 (mmmm) REVERT: M 17 GLU cc_start: 0.9579 (tm-30) cc_final: 0.9189 (pt0) REVERT: M 21 MET cc_start: 0.9034 (tmm) cc_final: 0.8819 (ppp) REVERT: M 47 GLU cc_start: 0.8873 (mp0) cc_final: 0.8405 (pm20) REVERT: J 153 ASP cc_start: 0.8966 (t0) cc_final: 0.8568 (p0) REVERT: J 188 MET cc_start: 0.9168 (mtm) cc_final: 0.8526 (mpp) REVERT: J 325 MET cc_start: 0.9127 (ptm) cc_final: 0.8801 (mpp) REVERT: J 337 LYS cc_start: 0.8661 (mttm) cc_final: 0.8059 (mttm) REVERT: N 47 GLU cc_start: 0.8699 (pm20) cc_final: 0.8433 (pm20) REVERT: K 15 LYS cc_start: 0.9902 (tptp) cc_final: 0.9674 (ptpp) REVERT: K 61 MET cc_start: 0.8618 (ppp) cc_final: 0.8104 (ppp) REVERT: K 71 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8238 (m) REVERT: K 111 TYR cc_start: 0.8934 (m-80) cc_final: 0.8640 (m-80) REVERT: K 142 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.8034 (p90) REVERT: K 153 ASP cc_start: 0.9055 (t0) cc_final: 0.8743 (p0) REVERT: K 325 MET cc_start: 0.8657 (mtp) cc_final: 0.8300 (mtp) REVERT: K 337 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8146 (mmmm) outliers start: 37 outliers final: 30 residues processed: 249 average time/residue: 0.3656 time to fit residues: 128.1786 Evaluate side-chains 250 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER 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 F residue 338 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 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 142 HIS 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 21 optimal weight: 6.9990 chunk 132 optimal weight: 0.0270 chunk 134 optimal weight: 1.9990 chunk 158 optimal weight: 0.2980 chunk 183 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.0644 ------------------------------------------------------------------------------- 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** ** I 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.074628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046367 restraints weight = 76323.242| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 5.39 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17464 Z= 0.122 Angle : 0.759 15.451 23636 Z= 0.381 Chirality : 0.044 0.212 2677 Planarity : 0.004 0.053 3060 Dihedral : 4.261 56.106 2384 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.98 % Allowed : 20.19 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2180 helix: -1.00 (0.28), residues: 326 sheet: 0.25 (0.20), residues: 707 loop : -1.68 (0.16), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.003 0.001 HIS C 156 PHE 0.013 0.001 PHE K 241 TYR 0.009 0.001 TYR F 264 ARG 0.021 0.000 ARG J 8 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 476) hydrogen bonds : angle 5.00711 ( 1341) covalent geometry : bond 0.00282 (17464) covalent geometry : angle 0.75870 (23636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8664.79 seconds wall clock time: 149 minutes 50.92 seconds (8990.92 seconds total)