Starting phenix.real_space_refine on Thu Mar 5 12:03:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eko_31171/03_2026/7eko_31171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eko_31171/03_2026/7eko_31171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eko_31171/03_2026/7eko_31171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eko_31171/03_2026/7eko_31171.map" model { file = "/net/cci-nas-00/data/ceres_data/7eko_31171/03_2026/7eko_31171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eko_31171/03_2026/7eko_31171.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 153 5.16 5 C 14214 2.51 5 N 3853 2.21 5 O 4250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22470 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1728 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain: "B" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1477 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain: "C" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1329 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1477 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain: "E" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1329 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "F" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1307 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "G" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1369 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain: "H" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1131 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "I" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1745 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "J" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1279 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain: "K" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1841 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 14, 'TRANS': 218} Chain: "L" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1494 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain: "M" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1014 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "N" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2691 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 23, 'TRANS': 314} Chain: "O" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1259 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 4, 'TRANS': 157} Time building chain proxies: 5.08, per 1000 atoms: 0.23 Number of scatterers: 22470 At special positions: 0 Unit cell: (166.068, 123.892, 122.574, 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 153 16.00 O 4250 8.00 N 3853 7.00 C 14214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 804.5 milliseconds 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5316 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 35 sheets defined 53.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 49 through 67 Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.508A pdb=" N LEU A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 171 Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.557A pdb=" N VAL A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 60 Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'B' and resid 103 through 117 Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 166 through 192 Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 34 through 52 removed outlier: 3.743A pdb=" N ASP C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 81 removed outlier: 3.655A pdb=" N CYS C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 103 Processing helix chain 'C' and resid 130 through 156 Processing helix chain 'C' and resid 158 through 168 removed outlier: 4.456A pdb=" N ARG C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'D' and resid 43 through 59 Processing helix chain 'D' and resid 70 through 88 removed outlier: 3.710A pdb=" N ASP D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 117 Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 166 through 192 Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 34 through 52 Processing helix chain 'E' and resid 67 through 79 Processing helix chain 'E' and resid 96 through 103 Processing helix chain 'E' and resid 129 through 155 Processing helix chain 'E' and resid 158 through 167 removed outlier: 3.516A pdb=" N ILE E 162 " --> pdb=" O PRO E 158 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 70 through 88 Processing helix chain 'F' and resid 103 through 117 Processing helix chain 'F' and resid 132 through 139 Processing helix chain 'F' and resid 165 through 192 Processing helix chain 'F' and resid 194 through 204 removed outlier: 3.892A pdb=" N ARG F 204 " --> pdb=" O LYS F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 34 through 52 Processing helix chain 'G' and resid 67 through 81 Processing helix chain 'G' and resid 96 through 103 Processing helix chain 'G' and resid 130 through 156 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 173 through 181 Processing helix chain 'H' and resid 358 through 372 removed outlier: 3.504A pdb=" N GLY H 362 " --> pdb=" O SER H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 394 Processing helix chain 'H' and resid 420 through 447 Processing helix chain 'H' and resid 449 through 457 Processing helix chain 'H' and resid 464 through 472 Processing helix chain 'H' and resid 479 through 492 removed outlier: 4.000A pdb=" N MET H 483 " --> pdb=" O THR H 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 20 Processing helix chain 'I' and resid 21 through 23 No H-bonds generated for 'chain 'I' and resid 21 through 23' Processing helix chain 'I' and resid 27 through 35 Processing helix chain 'I' and resid 45 through 60 Processing helix chain 'I' and resid 89 through 102 removed outlier: 4.335A pdb=" N PHE I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 125 Processing helix chain 'I' and resid 152 through 179 Processing helix chain 'I' and resid 181 through 189 Processing helix chain 'I' and resid 197 through 204 Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'J' and resid 358 through 372 removed outlier: 3.684A pdb=" N ILE J 372 " --> pdb=" O ALA J 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 394 Processing helix chain 'J' and resid 420 through 447 Processing helix chain 'J' and resid 449 through 459 removed outlier: 3.548A pdb=" N ARG J 459 " --> pdb=" O ARG J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 472 Processing helix chain 'J' and resid 479 through 509 removed outlier: 4.036A pdb=" N TYR J 496 " --> pdb=" O GLN J 492 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N HIS J 497 " --> pdb=" O VAL J 493 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 Processing helix chain 'K' and resid 19 through 27 Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.595A pdb=" N ALA K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 93 removed outlier: 3.532A pdb=" N ILE K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 142 through 144 No H-bonds generated for 'chain 'K' and resid 142 through 144' Processing helix chain 'K' and resid 145 through 169 removed outlier: 3.602A pdb=" N ARG K 150 " --> pdb=" O ILE K 146 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS K 151 " --> pdb=" O ASP K 147 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU K 155 " --> pdb=" O LYS K 151 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 180 removed outlier: 4.032A pdb=" N THR K 180 " --> pdb=" O MET K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 194 Processing helix chain 'K' and resid 210 through 214 Processing helix chain 'L' and resid 53 through 60 Processing helix chain 'L' and resid 71 through 89 removed outlier: 3.707A pdb=" N ASP L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 117 Processing helix chain 'L' and resid 131 through 137 Processing helix chain 'L' and resid 166 through 193 removed outlier: 3.510A pdb=" N MET L 170 " --> pdb=" O GLN L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 204 removed outlier: 3.742A pdb=" N SER L 204 " --> pdb=" O ILE L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 217 Processing helix chain 'M' and resid 358 through 372 removed outlier: 3.878A pdb=" N ILE M 372 " --> pdb=" O ALA M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 394 removed outlier: 3.934A pdb=" N ALA M 391 " --> pdb=" O ALA M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 447 Processing helix chain 'M' and resid 449 through 458 Processing helix chain 'M' and resid 464 through 472 Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 37 through 54 Processing helix chain 'N' and resid 81 through 93 Processing helix chain 'N' and resid 107 through 115 Processing helix chain 'N' and resid 143 through 169 removed outlier: 3.541A pdb=" N VAL N 147 " --> pdb=" O GLN N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 181 removed outlier: 3.513A pdb=" N GLN N 181 " --> pdb=" O ASP N 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 195 Processing helix chain 'N' and resid 204 through 218 Processing helix chain 'N' and resid 225 through 261 removed outlier: 3.796A pdb=" N GLN N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 277 removed outlier: 3.522A pdb=" N ASN N 272 " --> pdb=" O ASN N 268 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN N 277 " --> pdb=" O MET N 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 283 removed outlier: 4.236A pdb=" N LEU N 283 " --> pdb=" O LYS N 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 1 through 5 Processing helix chain 'O' and resid 7 through 12 Processing helix chain 'O' and resid 16 through 33 Processing helix chain 'O' and resid 39 through 50 Processing helix chain 'O' and resid 53 through 63 Processing helix chain 'O' and resid 66 through 80 Processing helix chain 'O' and resid 96 through 113 Processing helix chain 'O' and resid 119 through 129 Processing helix chain 'O' and resid 137 through 141 removed outlier: 3.525A pdb=" N ASN O 141 " --> pdb=" O PRO O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45 removed outlier: 6.528A pdb=" N ILE A 72 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL A 103 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 105 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE A 76 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA A 107 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 45 removed outlier: 6.528A pdb=" N ILE A 72 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL A 103 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 105 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE A 76 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA A 107 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N TYR A 125 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR A 102 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N MET A 127 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA A 104 " --> pdb=" O MET A 127 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA A 126 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 143 removed outlier: 7.116A pdb=" N GLY A 139 " --> pdb=" O PHE I 150 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE I 150 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER A 141 " --> pdb=" O ARG I 148 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG I 148 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 66 removed outlier: 5.609A pdb=" N SER B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU B 128 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG B 152 " --> pdb=" O CYS B 125 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY B 127 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N MET B 154 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA B 129 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 155 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 206 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 66 removed outlier: 5.609A pdb=" N SER B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU B 128 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 165 Processing sheet with id=AA7, first strand: chain 'C' and resid 26 through 30 removed outlier: 5.837A pdb=" N SER C 63 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU C 92 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ARG C 116 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY C 91 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N MET C 118 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA C 93 " --> pdb=" O MET C 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 128 through 129 Processing sheet with id=AA9, first strand: chain 'D' and resid 62 through 66 removed outlier: 6.243A pdb=" N VAL D 63 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASN D 98 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 65 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 12.569A pdb=" N ILE D 93 " --> pdb=" O CYS D 124 " (cutoff:3.500A) removed outlier: 13.530A pdb=" N ILE D 126 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N MET D 95 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N LEU D 128 " --> pdb=" O MET D 95 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL D 97 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA D 130 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER D 99 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N MET D 154 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA D 129 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 62 through 66 removed outlier: 6.243A pdb=" N VAL D 63 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASN D 98 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 65 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 12.569A pdb=" N ILE D 93 " --> pdb=" O CYS D 124 " (cutoff:3.500A) removed outlier: 13.530A pdb=" N ILE D 126 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N MET D 95 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N LEU D 128 " --> pdb=" O MET D 95 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL D 97 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA D 130 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER D 99 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N TYR D 146 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR D 123 " --> pdb=" O TYR D 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 159 through 165 removed outlier: 4.060A pdb=" N GLY M 419 " --> pdb=" O GLY D 160 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 26 through 30 removed outlier: 3.626A pdb=" N ASN E 62 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE E 57 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR E 88 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 59 " --> pdb=" O TYR E 88 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE E 61 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU E 92 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG E 116 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLY E 91 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N MET E 118 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA E 93 " --> pdb=" O MET E 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 26 through 30 removed outlier: 3.626A pdb=" N ASN E 62 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE E 57 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR E 88 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 59 " --> pdb=" O TYR E 88 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE E 61 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU E 92 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ASN E 110 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR E 87 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 62 through 66 removed outlier: 6.592A pdb=" N VAL F 63 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ASN F 98 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU F 65 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE F 93 " --> pdb=" O SER F 122 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N CYS F 124 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N MET F 95 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE F 126 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL F 97 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU F 128 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG F 152 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY F 127 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N MET F 154 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA F 129 " --> pdb=" O MET F 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 62 through 66 removed outlier: 6.592A pdb=" N VAL F 63 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ASN F 98 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU F 65 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE F 93 " --> pdb=" O SER F 122 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N CYS F 124 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N MET F 95 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE F 126 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL F 97 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU F 128 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA F 221 " --> pdb=" O ARG F 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 26 through 30 removed outlier: 6.203A pdb=" N ILE G 57 " --> pdb=" O ASN G 86 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N TYR G 88 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE G 59 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE G 61 " --> pdb=" O PHE G 90 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU G 92 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG G 116 " --> pdb=" O CYS G 89 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY G 91 " --> pdb=" O ARG G 116 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET G 118 " --> pdb=" O GLY G 91 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA G 93 " --> pdb=" O MET G 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 26 through 30 removed outlier: 6.203A pdb=" N ILE G 57 " --> pdb=" O ASN G 86 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N TYR G 88 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE G 59 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE G 61 " --> pdb=" O PHE G 90 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU G 92 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASN G 110 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N THR G 87 " --> pdb=" O ASN G 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.561A pdb=" N ALA G 126 " --> pdb=" O LEU J 417 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 347 through 354 removed outlier: 5.494A pdb=" N SER H 354 " --> pdb=" O LEU H 381 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL H 383 " --> pdb=" O SER H 354 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS H 407 " --> pdb=" O ALA H 380 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY H 382 " --> pdb=" O HIS H 407 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N MET H 409 " --> pdb=" O GLY H 382 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA H 384 " --> pdb=" O MET H 409 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 347 through 354 removed outlier: 5.494A pdb=" N SER H 354 " --> pdb=" O LEU H 381 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL H 383 " --> pdb=" O SER H 354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 37 through 40 removed outlier: 5.901A pdb=" N ILE I 70 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLY I 110 " --> pdb=" O ILE I 70 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL I 72 " --> pdb=" O GLY I 110 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR I 112 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU I 74 " --> pdb=" O THR I 112 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS I 114 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LYS I 138 " --> pdb=" O VAL I 111 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP I 113 " --> pdb=" O LYS I 138 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N SER I 140 " --> pdb=" O TRP I 113 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA I 115 " --> pdb=" O SER I 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 37 through 40 removed outlier: 5.901A pdb=" N ILE I 70 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLY I 110 " --> pdb=" O ILE I 70 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL I 72 " --> pdb=" O GLY I 110 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR I 112 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU I 74 " --> pdb=" O THR I 112 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS I 114 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N TYR I 132 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR I 109 " --> pdb=" O TYR I 132 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG I 131 " --> pdb=" O LYS I 209 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 348 through 354 removed outlier: 6.306A pdb=" N VAL J 348 " --> pdb=" O LEU J 377 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU J 379 " --> pdb=" O VAL J 348 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N MET J 350 " --> pdb=" O LEU J 379 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU J 381 " --> pdb=" O MET J 350 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE J 352 " --> pdb=" O LEU J 381 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL J 383 " --> pdb=" O ILE J 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER J 354 " --> pdb=" O VAL J 383 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 348 through 354 removed outlier: 6.306A pdb=" N VAL J 348 " --> pdb=" O LEU J 377 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU J 379 " --> pdb=" O VAL J 348 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N MET J 350 " --> pdb=" O LEU J 379 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU J 381 " --> pdb=" O MET J 350 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE J 352 " --> pdb=" O LEU J 381 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL J 383 " --> pdb=" O ILE J 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER J 354 " --> pdb=" O VAL J 383 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLY J 382 " --> pdb=" O THR J 403 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG J 400 " --> pdb=" O GLU J 476 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA J 478 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL J 402 " --> pdb=" O ALA J 478 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.227A pdb=" N ILE K 59 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU K 100 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE K 61 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL K 102 " --> pdb=" O PHE K 61 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE K 63 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASN K 104 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR K 128 " --> pdb=" O CYS K 101 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY K 103 " --> pdb=" O THR K 128 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N MET K 130 " --> pdb=" O GLY K 103 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA K 105 " --> pdb=" O MET K 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.227A pdb=" N ILE K 59 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU K 100 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE K 61 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL K 102 " --> pdb=" O PHE K 61 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE K 63 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASN K 104 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA K 122 " --> pdb=" O ILE K 97 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR K 99 " --> pdb=" O ALA K 122 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU K 124 " --> pdb=" O THR K 99 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N CYS K 101 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA K 123 " --> pdb=" O THR K 198 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AD1, first strand: chain 'L' and resid 64 through 66 removed outlier: 6.102A pdb=" N ILE L 93 " --> pdb=" O ALA L 122 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 128 through 130 removed outlier: 6.522A pdb=" N CYS L 129 " --> pdb=" O MET L 155 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 147 through 148 Processing sheet with id=AD4, first strand: chain 'M' and resid 348 through 354 removed outlier: 6.126A pdb=" N VAL M 348 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU M 379 " --> pdb=" O VAL M 348 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET M 350 " --> pdb=" O LEU M 379 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU M 381 " --> pdb=" O MET M 350 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE M 352 " --> pdb=" O LEU M 381 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL M 383 " --> pdb=" O ILE M 352 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N HIS M 407 " --> pdb=" O ALA M 380 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY M 382 " --> pdb=" O HIS M 407 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N MET M 409 " --> pdb=" O GLY M 382 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA M 384 " --> pdb=" O MET M 409 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 348 through 354 removed outlier: 6.126A pdb=" N VAL M 348 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU M 379 " --> pdb=" O VAL M 348 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET M 350 " --> pdb=" O LEU M 379 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU M 381 " --> pdb=" O MET M 350 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE M 352 " --> pdb=" O LEU M 381 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL M 383 " --> pdb=" O ILE M 352 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.106A pdb=" N ILE N 60 " --> pdb=" O SER N 98 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL N 100 " --> pdb=" O ILE N 60 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N MET N 62 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET N 102 " --> pdb=" O MET N 62 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE N 64 " --> pdb=" O MET N 102 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU N 104 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS N 122 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR N 99 " --> pdb=" O LYS N 122 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 129 through 131 Processing sheet with id=AD8, first strand: chain 'O' and resid 37 through 38 1273 hydrogen bonds defined for protein. 3726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6792 1.33 - 1.46: 4819 1.46 - 1.58: 11004 1.58 - 1.71: 0 1.71 - 1.83: 272 Bond restraints: 22887 Sorted by residual: bond pdb=" C GLY A 81 " pdb=" N GLN A 82 " ideal model delta sigma weight residual 1.327 1.266 0.061 1.61e-02 3.86e+03 1.43e+01 bond pdb=" N ILE K 59 " pdb=" CA ILE K 59 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.62e+00 bond pdb=" N GLN K 133 " pdb=" CA GLN K 133 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.16e-02 7.43e+03 9.56e+00 bond pdb=" N VAL G 193 " pdb=" CA VAL G 193 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.08e-02 8.57e+03 9.49e+00 bond pdb=" N VAL O 80 " pdb=" CA VAL O 80 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.15e+00 ... (remaining 22882 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 30576 3.57 - 7.14: 332 7.14 - 10.70: 18 10.70 - 14.27: 1 14.27 - 17.84: 2 Bond angle restraints: 30929 Sorted by residual: angle pdb=" C GLY N 170 " pdb=" N LEU N 171 " pdb=" CA LEU N 171 " ideal model delta sigma weight residual 120.97 138.81 -17.84 2.84e+00 1.24e-01 3.95e+01 angle pdb=" N LEU O 84 " pdb=" CA LEU O 84 " pdb=" C LEU O 84 " ideal model delta sigma weight residual 112.72 105.87 6.85 1.14e+00 7.69e-01 3.62e+01 angle pdb=" CB MET H 483 " pdb=" CG MET H 483 " pdb=" SD MET H 483 " ideal model delta sigma weight residual 112.70 95.79 16.91 3.00e+00 1.11e-01 3.18e+01 angle pdb=" N PRO K 56 " pdb=" CA PRO K 56 " pdb=" C PRO K 56 " ideal model delta sigma weight residual 114.68 109.09 5.59 1.04e+00 9.25e-01 2.89e+01 angle pdb=" N PRO K 58 " pdb=" CA PRO K 58 " pdb=" C PRO K 58 " ideal model delta sigma weight residual 111.22 118.12 -6.90 1.40e+00 5.10e-01 2.43e+01 ... (remaining 30924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 12883 23.98 - 47.95: 823 47.95 - 71.93: 148 71.93 - 95.90: 19 95.90 - 119.88: 1 Dihedral angle restraints: 13874 sinusoidal: 5564 harmonic: 8310 Sorted by residual: dihedral pdb=" CA PRO K 134 " pdb=" C PRO K 134 " pdb=" N LEU K 135 " pdb=" CA LEU K 135 " ideal model delta harmonic sigma weight residual -180.00 -60.12 -119.88 0 5.00e+00 4.00e-02 5.75e+02 dihedral pdb=" CA MET H 483 " pdb=" C MET H 483 " pdb=" N HIS H 484 " pdb=" CA HIS H 484 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ILE F 223 " pdb=" C ILE F 223 " pdb=" N SER F 224 " pdb=" CA SER F 224 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 13871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2962 0.079 - 0.159: 418 0.159 - 0.238: 55 0.238 - 0.317: 5 0.317 - 0.396: 3 Chirality restraints: 3443 Sorted by residual: chirality pdb=" CG LEU J 417 " pdb=" CB LEU J 417 " pdb=" CD1 LEU J 417 " pdb=" CD2 LEU J 417 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA VAL L 124 " pdb=" N VAL L 124 " pdb=" C VAL L 124 " pdb=" CB VAL L 124 " both_signs ideal model delta sigma weight residual False 2.44 2.78 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA GLU A 25 " pdb=" N GLU A 25 " pdb=" C GLU A 25 " pdb=" CB GLU A 25 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3440 not shown) Planarity restraints: 4017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 110 " 0.028 2.00e-02 2.50e+03 5.57e-02 3.11e+01 pdb=" C SER A 110 " -0.096 2.00e-02 2.50e+03 pdb=" O SER A 110 " 0.034 2.00e-02 2.50e+03 pdb=" N TYR A 111 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 52 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO E 53 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO E 53 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 53 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 223 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ILE F 223 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE F 223 " 0.024 2.00e-02 2.50e+03 pdb=" N SER F 224 " 0.021 2.00e-02 2.50e+03 ... (remaining 4014 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 440 2.68 - 3.23: 22304 3.23 - 3.79: 35651 3.79 - 4.34: 47994 4.34 - 4.90: 79458 Nonbonded interactions: 185847 Sorted by model distance: nonbonded pdb=" OH TYR I 195 " pdb=" OE2 GLU J 430 " model vdw 2.119 3.040 nonbonded pdb=" O SER L 163 " pdb=" NH1 ARG L 164 " model vdw 2.120 3.120 nonbonded pdb=" OG SER A 141 " pdb=" CB ALA I 156 " model vdw 2.127 3.460 nonbonded pdb=" OD1 ASN C 146 " pdb=" NH2 ARG C 149 " model vdw 2.129 3.120 nonbonded pdb=" OE1 GLN C 121 " pdb=" NZ LYS C 144 " model vdw 2.134 3.120 ... (remaining 185842 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 'B' and resid 54 through 225) selection = (chain 'D' and resid 54 through 225) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'E' selection = (chain 'G' and resid 17 through 190) } ncs_group { reference = (chain 'H' and resid 346 through 478) selection = (chain 'J' and resid 346 through 478) selection = chain 'M' } 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.870 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 22887 Z= 0.441 Angle : 0.987 17.838 30929 Z= 0.590 Chirality : 0.058 0.396 3443 Planarity : 0.005 0.113 4017 Dihedral : 15.699 119.881 8558 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.08 % Favored : 93.85 % Rotamer: Outliers : 2.55 % Allowed : 1.67 % Favored : 95.78 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.15), residues: 2860 helix: 0.16 (0.13), residues: 1536 sheet: -0.91 (0.31), residues: 282 loop : -1.69 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 218 TYR 0.030 0.003 TYR K 149 PHE 0.028 0.003 PHE I 196 TRP 0.010 0.002 TRP K 225 HIS 0.020 0.003 HIS H 484 Details of bonding type rmsd covalent geometry : bond 0.00906 (22887) covalent geometry : angle 0.98684 (30929) hydrogen bonds : bond 0.14399 ( 1226) hydrogen bonds : angle 6.90578 ( 3726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 518 time to evaluate : 0.891 Fit side-chains REVERT: A 138 MET cc_start: 0.7430 (mmt) cc_final: 0.6851 (mmt) REVERT: E 78 MET cc_start: 0.8592 (mtm) cc_final: 0.7991 (mtm) REVERT: E 141 MET cc_start: 0.7651 (mmm) cc_final: 0.7445 (mmt) REVERT: E 161 LYS cc_start: 0.6856 (pttp) cc_final: 0.6247 (mttt) REVERT: F 207 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5403 (t80) REVERT: G 34 GLU cc_start: 0.6139 (OUTLIER) cc_final: 0.5718 (pm20) REVERT: G 163 GLU cc_start: 0.6260 (mm-30) cc_final: 0.5477 (pt0) REVERT: G 180 TYR cc_start: 0.7744 (t80) cc_final: 0.7515 (t80) REVERT: H 460 ASP cc_start: 0.7476 (m-30) cc_final: 0.7229 (m-30) REVERT: I 183 GLU cc_start: 0.8138 (tp30) cc_final: 0.7756 (tp30) REVERT: J 464 THR cc_start: 0.6401 (m) cc_final: 0.6199 (m) REVERT: J 468 THR cc_start: 0.8649 (m) cc_final: 0.8407 (m) REVERT: K 108 GLU cc_start: 0.6207 (mp0) cc_final: 0.5903 (mp0) REVERT: K 155 GLU cc_start: 0.4788 (tt0) cc_final: 0.4173 (tt0) REVERT: K 169 LYS cc_start: 0.6287 (OUTLIER) cc_final: 0.5866 (pttp) REVERT: L 132 MET cc_start: 0.8126 (mmp) cc_final: 0.7800 (mmm) REVERT: L 216 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6482 (tm-30) REVERT: N 23 LEU cc_start: 0.8647 (tp) cc_final: 0.8240 (tp) REVERT: O 94 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7262 (ttpp) REVERT: O 145 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6034 (mp0) outliers start: 61 outliers final: 8 residues processed: 555 average time/residue: 0.1723 time to fit residues: 144.5865 Evaluate side-chains 459 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 447 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain K residue 169 LYS Chi-restraints excluded: chain M residue 428 SER Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 94 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS C 157 GLN D 51 GLN D 165 GLN E 110 ASN F 156 HIS F 174 ASN G 44 GLN G 120 HIS G 121 GLN H 361 ASN I 136 HIS J 497 HIS ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN L 190 ASN L 206 ASN M 451 HIS N 229 GLN O 113 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.160028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.131130 restraints weight = 26560.958| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.57 r_work: 0.3295 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22887 Z= 0.143 Angle : 0.627 9.809 30929 Z= 0.326 Chirality : 0.042 0.186 3443 Planarity : 0.005 0.090 4017 Dihedral : 5.866 57.152 3180 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.75 % Allowed : 8.39 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 2860 helix: 1.01 (0.13), residues: 1548 sheet: -0.52 (0.34), residues: 224 loop : -1.32 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 247 TYR 0.030 0.002 TYR E 154 PHE 0.021 0.002 PHE I 102 TRP 0.010 0.001 TRP N 108 HIS 0.013 0.001 HIS J 411 Details of bonding type rmsd covalent geometry : bond 0.00320 (22887) covalent geometry : angle 0.62665 (30929) hydrogen bonds : bond 0.04405 ( 1226) hydrogen bonds : angle 4.78155 ( 3726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 484 time to evaluate : 0.837 Fit side-chains REVERT: A 164 ARG cc_start: 0.8874 (mpt180) cc_final: 0.7968 (mmm-85) REVERT: B 88 ASP cc_start: 0.7763 (t0) cc_final: 0.7445 (t0) REVERT: B 170 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: C 149 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8186 (ttp80) REVERT: E 78 MET cc_start: 0.8521 (mtm) cc_final: 0.8184 (mtm) REVERT: F 83 TYR cc_start: 0.7603 (t80) cc_final: 0.7367 (t80) REVERT: F 207 PHE cc_start: 0.5899 (OUTLIER) cc_final: 0.5154 (t80) REVERT: G 151 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6849 (mtp) REVERT: G 157 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7269 (mm-40) REVERT: G 163 GLU cc_start: 0.6149 (mm-30) cc_final: 0.5172 (pt0) REVERT: H 350 MET cc_start: 0.8761 (ttt) cc_final: 0.8470 (ttt) REVERT: H 455 ARG cc_start: 0.6852 (ttp80) cc_final: 0.6160 (mmp80) REVERT: H 460 ASP cc_start: 0.7684 (m-30) cc_final: 0.7480 (m-30) REVERT: H 483 MET cc_start: 0.4476 (OUTLIER) cc_final: 0.4222 (ptt) REVERT: I 158 LEU cc_start: 0.7381 (mp) cc_final: 0.7086 (mt) REVERT: I 183 GLU cc_start: 0.8181 (tp30) cc_final: 0.7800 (tp30) REVERT: J 407 HIS cc_start: 0.6219 (m90) cc_final: 0.5598 (m-70) REVERT: J 468 THR cc_start: 0.8651 (m) cc_final: 0.8449 (m) REVERT: J 480 ASN cc_start: 0.7738 (m-40) cc_final: 0.7420 (m-40) REVERT: K 108 GLU cc_start: 0.6627 (mp0) cc_final: 0.6347 (mp0) REVERT: K 193 TYR cc_start: 0.6283 (t80) cc_final: 0.5966 (t80) REVERT: L 132 MET cc_start: 0.8363 (mmp) cc_final: 0.7938 (mmm) REVERT: L 209 MET cc_start: 0.8682 (mtm) cc_final: 0.8419 (mtt) REVERT: L 216 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6404 (tm-30) REVERT: N 23 LEU cc_start: 0.8456 (tp) cc_final: 0.8169 (tp) REVERT: N 209 GLU cc_start: 0.7833 (tp30) cc_final: 0.7432 (tp30) REVERT: N 213 GLN cc_start: 0.8597 (mt0) cc_final: 0.8344 (mt0) REVERT: O 51 GLU cc_start: 0.6665 (mm-30) cc_final: 0.5928 (mt-10) REVERT: O 148 ARG cc_start: 0.6035 (tmt-80) cc_final: 0.5433 (ttt90) outliers start: 42 outliers final: 23 residues processed: 507 average time/residue: 0.1584 time to fit residues: 125.1047 Evaluate side-chains 475 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 448 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 40 optimal weight: 0.0170 chunk 99 optimal weight: 4.9990 chunk 275 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN G 120 HIS H 411 HIS I 85 GLN J 497 HIS ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN N 229 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.159613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130034 restraints weight = 26690.386| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.60 r_work: 0.3287 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22887 Z= 0.143 Angle : 0.584 7.779 30929 Z= 0.302 Chirality : 0.042 0.162 3443 Planarity : 0.005 0.069 4017 Dihedral : 5.205 55.058 3164 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.92 % Allowed : 11.23 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 2860 helix: 1.36 (0.13), residues: 1550 sheet: -0.26 (0.34), residues: 230 loop : -1.20 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 271 TYR 0.028 0.002 TYR C 154 PHE 0.021 0.001 PHE I 102 TRP 0.012 0.001 TRP O 112 HIS 0.011 0.001 HIS H 484 Details of bonding type rmsd covalent geometry : bond 0.00331 (22887) covalent geometry : angle 0.58394 (30929) hydrogen bonds : bond 0.03819 ( 1226) hydrogen bonds : angle 4.36686 ( 3726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 493 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 164 ARG cc_start: 0.8937 (mpt180) cc_final: 0.8095 (mmm-85) REVERT: A 174 GLN cc_start: 0.7528 (pm20) cc_final: 0.5919 (tt0) REVERT: A 199 ASP cc_start: 0.8560 (m-30) cc_final: 0.8326 (m-30) REVERT: B 88 ASP cc_start: 0.7894 (t0) cc_final: 0.7551 (t0) REVERT: B 170 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: B 215 GLU cc_start: 0.6936 (mt-10) cc_final: 0.5883 (mt-10) REVERT: B 223 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8711 (mt) REVERT: C 149 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8212 (ttp80) REVERT: D 70 ASP cc_start: 0.8328 (p0) cc_final: 0.8110 (p0) REVERT: E 78 MET cc_start: 0.8507 (mtm) cc_final: 0.8240 (mtm) REVERT: E 112 MET cc_start: 0.7850 (mmp) cc_final: 0.7547 (mmt) REVERT: E 161 LYS cc_start: 0.7035 (ptmm) cc_final: 0.6812 (ptmt) REVERT: F 195 MET cc_start: 0.6788 (mmt) cc_final: 0.6461 (mmm) REVERT: F 207 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5850 (t80) REVERT: F 220 ASP cc_start: 0.7298 (m-30) cc_final: 0.6837 (m-30) REVERT: G 72 MET cc_start: 0.8522 (mmt) cc_final: 0.8030 (mmt) REVERT: G 151 MET cc_start: 0.7740 (mtp) cc_final: 0.6786 (mtp) REVERT: G 176 GLU cc_start: 0.7706 (tt0) cc_final: 0.7458 (tt0) REVERT: H 455 ARG cc_start: 0.7158 (ttp80) cc_final: 0.6272 (mmt180) REVERT: H 466 MET cc_start: 0.8589 (mmp) cc_final: 0.8381 (mmm) REVERT: H 489 MET cc_start: 0.6474 (mtp) cc_final: 0.5896 (mtm) REVERT: I 158 LEU cc_start: 0.7481 (mp) cc_final: 0.7274 (mt) REVERT: J 468 THR cc_start: 0.8616 (m) cc_final: 0.8396 (m) REVERT: J 480 ASN cc_start: 0.7616 (m-40) cc_final: 0.7271 (m-40) REVERT: K 34 MET cc_start: 0.8020 (ptm) cc_final: 0.7615 (ptp) REVERT: K 155 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.5159 (mm-30) REVERT: K 193 TYR cc_start: 0.6319 (t80) cc_final: 0.5955 (t80) REVERT: K 224 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6569 (tt) REVERT: L 170 MET cc_start: 0.6649 (mmm) cc_final: 0.5785 (mtt) REVERT: L 216 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6428 (tm-30) REVERT: M 433 LYS cc_start: 0.7438 (ttpp) cc_final: 0.7090 (ttpt) REVERT: N 94 LYS cc_start: 0.7051 (pttm) cc_final: 0.6254 (ptpp) REVERT: N 209 GLU cc_start: 0.7684 (tp30) cc_final: 0.7225 (tp30) REVERT: N 213 GLN cc_start: 0.8589 (mt0) cc_final: 0.8336 (mt0) REVERT: N 229 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7764 (pt0) REVERT: O 51 GLU cc_start: 0.6621 (mm-30) cc_final: 0.5944 (mt-10) REVERT: O 146 ARG cc_start: 0.6867 (ttt180) cc_final: 0.6565 (ttt-90) outliers start: 46 outliers final: 28 residues processed: 520 average time/residue: 0.1536 time to fit residues: 125.2120 Evaluate side-chains 498 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 464 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain M residue 428 SER Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 229 GLN Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 68 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 255 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN G 44 GLN G 120 HIS ** H 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 492 GLN ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN L 206 ASN M 429 GLN N 204 ASN N 229 GLN N 252 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.156848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127281 restraints weight = 26891.009| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.59 r_work: 0.3248 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22887 Z= 0.227 Angle : 0.642 8.755 30929 Z= 0.331 Chirality : 0.044 0.150 3443 Planarity : 0.005 0.061 4017 Dihedral : 5.269 53.528 3161 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.88 % Allowed : 13.78 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2860 helix: 1.31 (0.13), residues: 1551 sheet: -0.25 (0.33), residues: 234 loop : -1.31 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 118 TYR 0.030 0.002 TYR C 154 PHE 0.020 0.002 PHE I 102 TRP 0.010 0.002 TRP K 11 HIS 0.026 0.002 HIS H 484 Details of bonding type rmsd covalent geometry : bond 0.00539 (22887) covalent geometry : angle 0.64181 (30929) hydrogen bonds : bond 0.04164 ( 1226) hydrogen bonds : angle 4.43682 ( 3726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 461 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 ARG cc_start: 0.8889 (mpt180) cc_final: 0.7994 (mmm-85) REVERT: B 170 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: B 215 GLU cc_start: 0.6895 (mt-10) cc_final: 0.5762 (mt-10) REVERT: D 118 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7273 (mtm-85) REVERT: E 112 MET cc_start: 0.7827 (mmp) cc_final: 0.7608 (mmt) REVERT: F 207 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.5996 (t80) REVERT: F 220 ASP cc_start: 0.7352 (m-30) cc_final: 0.6883 (m-30) REVERT: G 101 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8643 (tp) REVERT: G 151 MET cc_start: 0.7645 (mtp) cc_final: 0.6803 (mtp) REVERT: G 176 GLU cc_start: 0.7885 (tt0) cc_final: 0.7652 (tt0) REVERT: H 350 MET cc_start: 0.8735 (ttt) cc_final: 0.8435 (ttt) REVERT: H 489 MET cc_start: 0.6526 (mtp) cc_final: 0.5943 (mtm) REVERT: I 158 LEU cc_start: 0.7516 (mp) cc_final: 0.7223 (mt) REVERT: J 468 THR cc_start: 0.8763 (m) cc_final: 0.8486 (m) REVERT: J 480 ASN cc_start: 0.7633 (m-40) cc_final: 0.7291 (m-40) REVERT: K 34 MET cc_start: 0.8064 (ptm) cc_final: 0.7661 (ptp) REVERT: K 112 LEU cc_start: 0.8491 (mt) cc_final: 0.8274 (mp) REVERT: K 136 GLN cc_start: 0.4336 (OUTLIER) cc_final: 0.3907 (mp10) REVERT: K 155 GLU cc_start: 0.5759 (OUTLIER) cc_final: 0.5189 (mm-30) REVERT: K 193 TYR cc_start: 0.6289 (t80) cc_final: 0.5927 (t80) REVERT: L 216 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6416 (tm-30) REVERT: M 433 LYS cc_start: 0.7471 (ttpp) cc_final: 0.7183 (ttpp) REVERT: N 94 LYS cc_start: 0.7284 (pttm) cc_final: 0.7026 (pttm) REVERT: N 209 GLU cc_start: 0.7794 (tp30) cc_final: 0.7291 (tp30) REVERT: N 213 GLN cc_start: 0.8692 (mt0) cc_final: 0.8443 (mt0) REVERT: O 51 GLU cc_start: 0.6272 (mt-10) cc_final: 0.5825 (mm-30) outliers start: 69 outliers final: 51 residues processed: 502 average time/residue: 0.1636 time to fit residues: 127.2492 Evaluate side-chains 511 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 455 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 396 THR Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 428 SER Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 216 optimal weight: 3.9990 chunk 178 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 224 optimal weight: 6.9990 chunk 168 optimal weight: 0.0370 chunk 186 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 HIS E 110 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN G 44 GLN G 120 HIS H 411 HIS J 492 GLN ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.160118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.130591 restraints weight = 26497.221| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.59 r_work: 0.3292 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22887 Z= 0.125 Angle : 0.554 7.104 30929 Z= 0.286 Chirality : 0.041 0.143 3443 Planarity : 0.004 0.055 4017 Dihedral : 4.955 51.305 3161 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.59 % Allowed : 15.32 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.16), residues: 2860 helix: 1.65 (0.13), residues: 1553 sheet: -0.22 (0.34), residues: 232 loop : -1.25 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 271 TYR 0.022 0.001 TYR L 196 PHE 0.015 0.001 PHE I 102 TRP 0.009 0.001 TRP O 112 HIS 0.023 0.001 HIS H 484 Details of bonding type rmsd covalent geometry : bond 0.00285 (22887) covalent geometry : angle 0.55363 (30929) hydrogen bonds : bond 0.03494 ( 1226) hydrogen bonds : angle 4.16333 ( 3726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 480 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 ARG cc_start: 0.8933 (mpt180) cc_final: 0.8111 (mmm-85) REVERT: A 174 GLN cc_start: 0.7582 (pm20) cc_final: 0.6018 (tt0) REVERT: B 88 ASP cc_start: 0.7882 (t0) cc_final: 0.7659 (t0) REVERT: B 92 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: B 170 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: B 215 GLU cc_start: 0.6954 (mt-10) cc_final: 0.5949 (mt-10) REVERT: C 149 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8219 (ttp80) REVERT: D 118 ARG cc_start: 0.7548 (mtm-85) cc_final: 0.6688 (mtt90) REVERT: D 200 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8443 (ttpp) REVERT: D 211 GLN cc_start: 0.3995 (mm110) cc_final: 0.3732 (mp10) REVERT: F 220 ASP cc_start: 0.7337 (m-30) cc_final: 0.6951 (m-30) REVERT: G 43 SER cc_start: 0.7654 (t) cc_final: 0.7258 (p) REVERT: G 151 MET cc_start: 0.7518 (mtp) cc_final: 0.6708 (mtp) REVERT: G 176 GLU cc_start: 0.7822 (tt0) cc_final: 0.7574 (tt0) REVERT: H 350 MET cc_start: 0.8784 (ttt) cc_final: 0.8519 (ttt) REVERT: H 444 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8730 (tt) REVERT: H 455 ARG cc_start: 0.7114 (ttp80) cc_final: 0.6225 (mmt180) REVERT: H 489 MET cc_start: 0.6488 (mtp) cc_final: 0.5914 (mtm) REVERT: I 158 LEU cc_start: 0.7472 (mp) cc_final: 0.7219 (mt) REVERT: J 468 THR cc_start: 0.8699 (m) cc_final: 0.8402 (m) REVERT: J 480 ASN cc_start: 0.7640 (m-40) cc_final: 0.7297 (m-40) REVERT: K 34 MET cc_start: 0.8108 (ptm) cc_final: 0.7716 (ptp) REVERT: K 92 GLN cc_start: 0.7268 (mt0) cc_final: 0.7005 (mt0) REVERT: K 136 GLN cc_start: 0.4135 (OUTLIER) cc_final: 0.3682 (mp10) REVERT: K 155 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.5071 (mm-30) REVERT: K 193 TYR cc_start: 0.6255 (t80) cc_final: 0.5977 (t80) REVERT: L 128 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8475 (pp) REVERT: L 216 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6402 (tm-30) REVERT: M 433 LYS cc_start: 0.7291 (ttpp) cc_final: 0.6963 (ttpt) REVERT: N 23 LEU cc_start: 0.8541 (tp) cc_final: 0.8225 (tp) REVERT: N 77 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7944 (pp) REVERT: N 94 LYS cc_start: 0.7030 (pttm) cc_final: 0.6812 (pttm) REVERT: N 164 MET cc_start: 0.8757 (mmm) cc_final: 0.8370 (mtt) REVERT: N 209 GLU cc_start: 0.7624 (tp30) cc_final: 0.7314 (tp30) REVERT: N 213 GLN cc_start: 0.8539 (mt0) cc_final: 0.8236 (mt0) REVERT: O 51 GLU cc_start: 0.6291 (mt-10) cc_final: 0.5838 (mm-30) outliers start: 62 outliers final: 43 residues processed: 514 average time/residue: 0.1665 time to fit residues: 131.4943 Evaluate side-chains 499 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 449 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 396 THR Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain H residue 483 MET Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain M residue 428 SER Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 21 optimal weight: 0.0970 chunk 171 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN H 411 HIS J 492 GLN ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.160121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.130547 restraints weight = 26755.793| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.60 r_work: 0.3288 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22887 Z= 0.131 Angle : 0.557 8.679 30929 Z= 0.286 Chirality : 0.041 0.170 3443 Planarity : 0.004 0.060 4017 Dihedral : 4.769 51.437 3159 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.55 % Allowed : 16.28 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.16), residues: 2860 helix: 1.76 (0.13), residues: 1554 sheet: -0.11 (0.34), residues: 232 loop : -1.20 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 247 TYR 0.021 0.001 TYR L 196 PHE 0.013 0.001 PHE J 371 TRP 0.007 0.001 TRP N 151 HIS 0.014 0.001 HIS J 407 Details of bonding type rmsd covalent geometry : bond 0.00307 (22887) covalent geometry : angle 0.55732 (30929) hydrogen bonds : bond 0.03445 ( 1226) hydrogen bonds : angle 4.11152 ( 3726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 452 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 164 ARG cc_start: 0.8922 (mpt180) cc_final: 0.8119 (mmm-85) REVERT: A 174 GLN cc_start: 0.7595 (pm20) cc_final: 0.6060 (tt0) REVERT: B 170 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: B 215 GLU cc_start: 0.6965 (mt-10) cc_final: 0.5950 (mt-10) REVERT: C 149 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.8235 (ttp80) REVERT: D 51 GLN cc_start: 0.5174 (mp10) cc_final: 0.4838 (mp10) REVERT: D 118 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.6756 (mtt90) REVERT: D 200 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8460 (ttpp) REVERT: F 220 ASP cc_start: 0.7336 (m-30) cc_final: 0.6941 (m-30) REVERT: G 101 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8570 (tp) REVERT: G 151 MET cc_start: 0.7520 (mtp) cc_final: 0.6743 (mtp) REVERT: G 176 GLU cc_start: 0.7803 (tt0) cc_final: 0.7582 (tt0) REVERT: H 350 MET cc_start: 0.8686 (ttt) cc_final: 0.8413 (ttt) REVERT: H 444 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8737 (tt) REVERT: H 455 ARG cc_start: 0.7134 (ttp80) cc_final: 0.6242 (mmt180) REVERT: H 489 MET cc_start: 0.6416 (mtp) cc_final: 0.5846 (mtm) REVERT: I 158 LEU cc_start: 0.7480 (mp) cc_final: 0.7257 (mt) REVERT: I 222 MET cc_start: 0.5040 (ptp) cc_final: 0.2473 (tpp) REVERT: J 468 THR cc_start: 0.8709 (m) cc_final: 0.8396 (m) REVERT: J 480 ASN cc_start: 0.7598 (m-40) cc_final: 0.7269 (m-40) REVERT: K 34 MET cc_start: 0.8117 (ptm) cc_final: 0.7742 (ptp) REVERT: K 92 GLN cc_start: 0.7274 (mt0) cc_final: 0.7036 (mt0) REVERT: K 136 GLN cc_start: 0.4264 (OUTLIER) cc_final: 0.3750 (mp10) REVERT: K 155 GLU cc_start: 0.5623 (OUTLIER) cc_final: 0.5086 (mm-30) REVERT: K 193 TYR cc_start: 0.6264 (t80) cc_final: 0.5989 (t80) REVERT: K 224 LEU cc_start: 0.6680 (tt) cc_final: 0.6408 (tt) REVERT: L 128 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8472 (pp) REVERT: L 216 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6424 (tm-30) REVERT: M 432 MET cc_start: 0.8103 (mmp) cc_final: 0.7841 (mmm) REVERT: N 77 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7957 (pp) REVERT: N 164 MET cc_start: 0.8742 (mmm) cc_final: 0.8434 (mtt) REVERT: N 209 GLU cc_start: 0.7575 (tp30) cc_final: 0.7362 (tp30) REVERT: O 51 GLU cc_start: 0.6295 (mt-10) cc_final: 0.5860 (mm-30) outliers start: 61 outliers final: 41 residues processed: 486 average time/residue: 0.1670 time to fit residues: 124.0861 Evaluate side-chains 495 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 447 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 396 THR Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain M residue 428 SER Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 67 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 258 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 199 optimal weight: 0.0980 chunk 210 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN H 411 HIS J 492 GLN ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.160655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.132486 restraints weight = 26567.687| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.48 r_work: 0.3316 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22887 Z= 0.114 Angle : 0.538 7.937 30929 Z= 0.276 Chirality : 0.041 0.168 3443 Planarity : 0.004 0.053 4017 Dihedral : 4.651 51.063 3158 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.05 % Allowed : 15.78 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.16), residues: 2860 helix: 1.90 (0.13), residues: 1555 sheet: -0.13 (0.33), residues: 238 loop : -1.09 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 247 TYR 0.019 0.001 TYR C 154 PHE 0.013 0.001 PHE J 371 TRP 0.007 0.001 TRP N 151 HIS 0.012 0.001 HIS J 407 Details of bonding type rmsd covalent geometry : bond 0.00261 (22887) covalent geometry : angle 0.53751 (30929) hydrogen bonds : bond 0.03267 ( 1226) hydrogen bonds : angle 4.00131 ( 3726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 459 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 133 MET cc_start: 0.8990 (tmm) cc_final: 0.8773 (ttt) REVERT: A 164 ARG cc_start: 0.8878 (mpt180) cc_final: 0.8070 (mmm-85) REVERT: A 174 GLN cc_start: 0.7594 (pm20) cc_final: 0.6093 (tt0) REVERT: B 170 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: B 215 GLU cc_start: 0.6904 (mt-10) cc_final: 0.5886 (mt-10) REVERT: C 118 MET cc_start: 0.8776 (ttt) cc_final: 0.8567 (ttt) REVERT: C 149 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8220 (ttp80) REVERT: D 118 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.6728 (mtt90) REVERT: D 200 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8474 (ttpp) REVERT: E 161 LYS cc_start: 0.7224 (ptmt) cc_final: 0.6114 (mttt) REVERT: F 220 ASP cc_start: 0.7261 (m-30) cc_final: 0.6864 (m-30) REVERT: G 101 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8527 (tp) REVERT: G 147 LEU cc_start: 0.7401 (mt) cc_final: 0.7097 (mp) REVERT: G 151 MET cc_start: 0.7516 (mtp) cc_final: 0.6726 (mtp) REVERT: G 176 GLU cc_start: 0.7750 (tt0) cc_final: 0.7513 (tt0) REVERT: H 350 MET cc_start: 0.8659 (ttt) cc_final: 0.8350 (ttt) REVERT: H 444 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8742 (tt) REVERT: H 466 MET cc_start: 0.8600 (mmp) cc_final: 0.8353 (mmm) REVERT: H 489 MET cc_start: 0.6223 (mtp) cc_final: 0.5631 (mtm) REVERT: I 158 LEU cc_start: 0.7431 (mp) cc_final: 0.7206 (mt) REVERT: I 222 MET cc_start: 0.4721 (ptp) cc_final: 0.2296 (tpp) REVERT: J 468 THR cc_start: 0.8640 (m) cc_final: 0.8308 (m) REVERT: J 480 ASN cc_start: 0.7634 (m-40) cc_final: 0.7288 (m-40) REVERT: K 34 MET cc_start: 0.8171 (ptm) cc_final: 0.7797 (ptp) REVERT: K 92 GLN cc_start: 0.7097 (mt0) cc_final: 0.6843 (mt0) REVERT: K 136 GLN cc_start: 0.4171 (OUTLIER) cc_final: 0.3639 (mp10) REVERT: K 155 GLU cc_start: 0.5505 (OUTLIER) cc_final: 0.4971 (mm-30) REVERT: K 193 TYR cc_start: 0.6235 (t80) cc_final: 0.5962 (t80) REVERT: K 224 LEU cc_start: 0.6632 (tt) cc_final: 0.6369 (tt) REVERT: L 128 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8454 (pp) REVERT: L 216 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6398 (tm-30) REVERT: M 433 LYS cc_start: 0.7524 (ttpt) cc_final: 0.7217 (ttpt) REVERT: M 467 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: N 94 LYS cc_start: 0.6771 (pttm) cc_final: 0.6187 (ptpp) REVERT: N 164 MET cc_start: 0.8703 (mmm) cc_final: 0.8429 (mtt) REVERT: O 51 GLU cc_start: 0.6366 (mt-10) cc_final: 0.6049 (mm-30) REVERT: O 146 ARG cc_start: 0.6771 (ttt180) cc_final: 0.6563 (ttt-90) outliers start: 73 outliers final: 51 residues processed: 492 average time/residue: 0.1640 time to fit residues: 124.8371 Evaluate side-chains 508 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 450 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 396 THR Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain J residue 350 MET Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain M residue 428 SER Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain M residue 467 GLU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 125 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 254 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 268 optimal weight: 0.6980 chunk 225 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 210 optimal weight: 0.8980 chunk 248 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 411 HIS ** H 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN L 61 GLN L 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.131514 restraints weight = 26390.222| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.60 r_work: 0.3316 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22887 Z= 0.114 Angle : 0.535 7.890 30929 Z= 0.274 Chirality : 0.041 0.253 3443 Planarity : 0.004 0.053 4017 Dihedral : 4.576 51.150 3158 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.92 % Allowed : 16.41 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.16), residues: 2860 helix: 1.98 (0.13), residues: 1556 sheet: -0.05 (0.34), residues: 234 loop : -1.03 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 104 TYR 0.028 0.001 TYR L 196 PHE 0.009 0.001 PHE J 371 TRP 0.007 0.001 TRP N 151 HIS 0.011 0.001 HIS J 407 Details of bonding type rmsd covalent geometry : bond 0.00263 (22887) covalent geometry : angle 0.53521 (30929) hydrogen bonds : bond 0.03210 ( 1226) hydrogen bonds : angle 3.95719 ( 3726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 459 time to evaluate : 0.836 Fit side-chains REVERT: A 133 MET cc_start: 0.9028 (tmm) cc_final: 0.8807 (ttt) REVERT: A 164 ARG cc_start: 0.8853 (mpt180) cc_final: 0.8029 (mmm-85) REVERT: A 174 GLN cc_start: 0.7567 (pm20) cc_final: 0.6070 (tt0) REVERT: A 199 ASP cc_start: 0.8426 (m-30) cc_final: 0.8057 (m-30) REVERT: B 170 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: B 215 GLU cc_start: 0.6856 (mt-10) cc_final: 0.5842 (mt-10) REVERT: C 149 ARG cc_start: 0.8469 (ttp-110) cc_final: 0.8211 (ttp80) REVERT: D 51 GLN cc_start: 0.5184 (mp10) cc_final: 0.4921 (mp10) REVERT: D 118 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.6754 (mtt90) REVERT: D 200 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8459 (ttpp) REVERT: E 161 LYS cc_start: 0.7171 (ptmt) cc_final: 0.6219 (mttt) REVERT: F 220 ASP cc_start: 0.7234 (m-30) cc_final: 0.6859 (m-30) REVERT: G 101 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8489 (tp) REVERT: G 147 LEU cc_start: 0.7256 (mt) cc_final: 0.6912 (mp) REVERT: G 151 MET cc_start: 0.7506 (mtp) cc_final: 0.6697 (mtp) REVERT: G 170 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7602 (ptm160) REVERT: H 350 MET cc_start: 0.8668 (ttt) cc_final: 0.8357 (ttt) REVERT: H 444 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8744 (tt) REVERT: H 466 MET cc_start: 0.8595 (mmp) cc_final: 0.8365 (mmm) REVERT: H 489 MET cc_start: 0.6176 (mtp) cc_final: 0.5649 (mtm) REVERT: I 158 LEU cc_start: 0.7367 (mp) cc_final: 0.7146 (mt) REVERT: I 222 MET cc_start: 0.4692 (ptp) cc_final: 0.2267 (tpp) REVERT: J 480 ASN cc_start: 0.7565 (m-40) cc_final: 0.7235 (m-40) REVERT: K 34 MET cc_start: 0.8233 (ptm) cc_final: 0.7842 (ptp) REVERT: K 92 GLN cc_start: 0.7076 (mt0) cc_final: 0.6826 (mt0) REVERT: K 136 GLN cc_start: 0.4247 (OUTLIER) cc_final: 0.3718 (mp10) REVERT: K 155 GLU cc_start: 0.5302 (OUTLIER) cc_final: 0.4314 (mt-10) REVERT: K 193 TYR cc_start: 0.6238 (t80) cc_final: 0.5869 (t80) REVERT: K 224 LEU cc_start: 0.6700 (tt) cc_final: 0.6415 (tt) REVERT: L 86 ASP cc_start: 0.7377 (m-30) cc_final: 0.6886 (m-30) REVERT: L 128 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8459 (pp) REVERT: L 216 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6355 (tm-30) REVERT: M 433 LYS cc_start: 0.7479 (ttpt) cc_final: 0.7247 (ttpp) REVERT: M 467 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: N 94 LYS cc_start: 0.6701 (pttm) cc_final: 0.6105 (ptpp) REVERT: N 209 GLU cc_start: 0.7715 (tp30) cc_final: 0.7507 (tp30) REVERT: O 51 GLU cc_start: 0.6330 (mt-10) cc_final: 0.6005 (mm-30) outliers start: 70 outliers final: 48 residues processed: 494 average time/residue: 0.1636 time to fit residues: 123.9700 Evaluate side-chains 497 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 442 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 396 THR Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain M residue 467 GLU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 125 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 262 optimal weight: 0.0050 chunk 256 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 GLN L 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.132326 restraints weight = 26612.379| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.56 r_work: 0.3315 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22887 Z= 0.122 Angle : 0.548 7.687 30929 Z= 0.281 Chirality : 0.041 0.282 3443 Planarity : 0.004 0.053 4017 Dihedral : 4.564 51.174 3158 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.26 % Allowed : 16.70 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.16), residues: 2860 helix: 2.00 (0.13), residues: 1556 sheet: -0.03 (0.34), residues: 234 loop : -1.00 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 49 TYR 0.025 0.001 TYR L 196 PHE 0.010 0.001 PHE M 355 TRP 0.006 0.001 TRP N 151 HIS 0.011 0.001 HIS J 407 Details of bonding type rmsd covalent geometry : bond 0.00282 (22887) covalent geometry : angle 0.54783 (30929) hydrogen bonds : bond 0.03219 ( 1226) hydrogen bonds : angle 3.94280 ( 3726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 448 time to evaluate : 0.820 Fit side-chains REVERT: A 164 ARG cc_start: 0.8850 (mpt180) cc_final: 0.8033 (mmm-85) REVERT: A 174 GLN cc_start: 0.7582 (pm20) cc_final: 0.6083 (tt0) REVERT: A 190 GLU cc_start: 0.7749 (mp0) cc_final: 0.7277 (mp0) REVERT: A 199 ASP cc_start: 0.8414 (m-30) cc_final: 0.8066 (m-30) REVERT: B 156 HIS cc_start: 0.8076 (p-80) cc_final: 0.7849 (p-80) REVERT: B 170 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: B 215 GLU cc_start: 0.6865 (mt-10) cc_final: 0.5836 (mt-10) REVERT: C 44 GLN cc_start: 0.8108 (mt0) cc_final: 0.7908 (mt0) REVERT: C 149 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.8218 (ttp80) REVERT: D 118 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.6770 (mtt90) REVERT: E 161 LYS cc_start: 0.7055 (ptmt) cc_final: 0.6114 (mttt) REVERT: F 220 ASP cc_start: 0.7214 (m-30) cc_final: 0.6839 (m-30) REVERT: G 101 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8501 (tp) REVERT: G 147 LEU cc_start: 0.7255 (mt) cc_final: 0.6921 (mp) REVERT: G 151 MET cc_start: 0.7581 (mtp) cc_final: 0.6777 (mtp) REVERT: G 170 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7560 (ptm160) REVERT: G 176 GLU cc_start: 0.7584 (tt0) cc_final: 0.7305 (tt0) REVERT: H 350 MET cc_start: 0.8667 (ttt) cc_final: 0.8371 (ttt) REVERT: H 444 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8770 (tt) REVERT: H 489 MET cc_start: 0.6165 (mtp) cc_final: 0.5605 (mtm) REVERT: I 158 LEU cc_start: 0.7367 (mp) cc_final: 0.7146 (mt) REVERT: I 222 MET cc_start: 0.4766 (ptp) cc_final: 0.2313 (tpp) REVERT: J 480 ASN cc_start: 0.7594 (m-40) cc_final: 0.7265 (m-40) REVERT: K 34 MET cc_start: 0.8274 (ptm) cc_final: 0.7875 (ptp) REVERT: K 92 GLN cc_start: 0.7086 (mt0) cc_final: 0.6848 (mt0) REVERT: K 136 GLN cc_start: 0.4365 (OUTLIER) cc_final: 0.3860 (mp10) REVERT: K 155 GLU cc_start: 0.5302 (OUTLIER) cc_final: 0.4307 (mt-10) REVERT: K 193 TYR cc_start: 0.6272 (t80) cc_final: 0.5903 (t80) REVERT: L 118 ARG cc_start: 0.7041 (ttp-110) cc_final: 0.6759 (mtm110) REVERT: L 128 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8460 (pp) REVERT: L 216 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6347 (tm-30) REVERT: M 432 MET cc_start: 0.7982 (mmp) cc_final: 0.7782 (mmm) REVERT: M 467 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7777 (mt-10) REVERT: N 94 LYS cc_start: 0.6669 (pttm) cc_final: 0.6074 (ptpp) outliers start: 78 outliers final: 58 residues processed: 489 average time/residue: 0.1641 time to fit residues: 124.6629 Evaluate side-chains 510 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 445 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain H residue 383 VAL Chi-restraints excluded: chain H residue 396 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain J residue 350 MET Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain M residue 428 SER Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain M residue 467 GLU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 125 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 170 optimal weight: 3.9990 chunk 133 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 HIS G 157 GLN J 492 GLN ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 GLN L 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.161529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.132128 restraints weight = 26595.664| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.56 r_work: 0.3313 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22887 Z= 0.119 Angle : 0.549 7.670 30929 Z= 0.282 Chirality : 0.041 0.145 3443 Planarity : 0.004 0.053 4017 Dihedral : 4.550 50.957 3158 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.88 % Allowed : 17.33 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.16), residues: 2860 helix: 2.04 (0.13), residues: 1555 sheet: -0.02 (0.34), residues: 234 loop : -0.98 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 23 TYR 0.025 0.001 TYR L 196 PHE 0.010 0.001 PHE M 355 TRP 0.009 0.001 TRP K 11 HIS 0.011 0.001 HIS J 407 Details of bonding type rmsd covalent geometry : bond 0.00278 (22887) covalent geometry : angle 0.54923 (30929) hydrogen bonds : bond 0.03221 ( 1226) hydrogen bonds : angle 3.93598 ( 3726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 447 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 164 ARG cc_start: 0.8870 (mpt180) cc_final: 0.8072 (mmm-85) REVERT: A 174 GLN cc_start: 0.7614 (pm20) cc_final: 0.6124 (tt0) REVERT: A 190 GLU cc_start: 0.7739 (mp0) cc_final: 0.7276 (mp0) REVERT: B 170 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: B 215 GLU cc_start: 0.6922 (mt-10) cc_final: 0.5916 (mt-10) REVERT: C 72 MET cc_start: 0.8983 (mmm) cc_final: 0.8368 (mmm) REVERT: C 149 ARG cc_start: 0.8466 (ttp-110) cc_final: 0.8243 (ttp80) REVERT: D 51 GLN cc_start: 0.5206 (mp10) cc_final: 0.4986 (mp10) REVERT: D 118 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.6787 (mtt90) REVERT: D 159 LEU cc_start: 0.8318 (mt) cc_final: 0.8059 (mt) REVERT: E 112 MET cc_start: 0.7997 (mmt) cc_final: 0.7773 (mmp) REVERT: E 118 MET cc_start: 0.8288 (ttp) cc_final: 0.7842 (tmm) REVERT: E 141 MET cc_start: 0.7980 (mmm) cc_final: 0.7579 (mmp) REVERT: E 161 LYS cc_start: 0.7099 (ptmt) cc_final: 0.6194 (mttt) REVERT: F 115 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.7161 (mtp85) REVERT: F 220 ASP cc_start: 0.7221 (m-30) cc_final: 0.6859 (m-30) REVERT: G 101 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8534 (tp) REVERT: G 147 LEU cc_start: 0.7269 (mt) cc_final: 0.6944 (mp) REVERT: G 151 MET cc_start: 0.7575 (mtp) cc_final: 0.6777 (mtp) REVERT: G 170 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7563 (ptm160) REVERT: G 176 GLU cc_start: 0.7596 (tt0) cc_final: 0.7335 (tt0) REVERT: H 350 MET cc_start: 0.8658 (ttt) cc_final: 0.8366 (ttt) REVERT: H 444 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8775 (tt) REVERT: H 489 MET cc_start: 0.6110 (mtp) cc_final: 0.5712 (mtm) REVERT: I 158 LEU cc_start: 0.7392 (mp) cc_final: 0.7185 (mt) REVERT: I 222 MET cc_start: 0.4766 (ptp) cc_final: 0.2294 (tpp) REVERT: J 480 ASN cc_start: 0.7615 (m-40) cc_final: 0.7282 (m-40) REVERT: K 34 MET cc_start: 0.8355 (ptm) cc_final: 0.7989 (ptp) REVERT: K 92 GLN cc_start: 0.7107 (mt0) cc_final: 0.6860 (mt0) REVERT: K 155 GLU cc_start: 0.5292 (OUTLIER) cc_final: 0.4311 (mt-10) REVERT: K 174 GLN cc_start: 0.7028 (mt0) cc_final: 0.6784 (mt0) REVERT: K 193 TYR cc_start: 0.6289 (t80) cc_final: 0.5925 (t80) REVERT: L 128 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8469 (pp) REVERT: L 216 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6362 (tm-30) REVERT: M 414 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7698 (mm-30) REVERT: M 467 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: N 94 LYS cc_start: 0.6636 (pttm) cc_final: 0.6065 (ptpp) REVERT: N 164 MET cc_start: 0.8687 (mmm) cc_final: 0.8445 (mtt) REVERT: O 51 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5572 (mt-10) outliers start: 69 outliers final: 58 residues processed: 484 average time/residue: 0.1731 time to fit residues: 128.6501 Evaluate side-chains 505 residues out of total 2395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 440 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain H residue 383 VAL Chi-restraints excluded: chain H residue 396 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain J residue 350 MET Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain M residue 467 GLU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain O residue 51 GLU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 125 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 226 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 492 GLN ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.160160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.130691 restraints weight = 26700.097| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.59 r_work: 0.3297 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22887 Z= 0.149 Angle : 0.574 9.792 30929 Z= 0.294 Chirality : 0.042 0.148 3443 Planarity : 0.004 0.053 4017 Dihedral : 4.622 51.083 3158 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.09 % Allowed : 17.49 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.16), residues: 2860 helix: 1.96 (0.13), residues: 1553 sheet: -0.00 (0.33), residues: 238 loop : -1.07 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 168 TYR 0.025 0.001 TYR L 196 PHE 0.014 0.001 PHE D 206 TRP 0.013 0.001 TRP K 11 HIS 0.012 0.001 HIS J 407 Details of bonding type rmsd covalent geometry : bond 0.00354 (22887) covalent geometry : angle 0.57383 (30929) hydrogen bonds : bond 0.03399 ( 1226) hydrogen bonds : angle 4.01793 ( 3726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6101.41 seconds wall clock time: 105 minutes 3.93 seconds (6303.93 seconds total)