Starting phenix.real_space_refine on Tue Aug 26 06:39:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ioj_35620/08_2025/8ioj_35620_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ioj_35620/08_2025/8ioj_35620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ioj_35620/08_2025/8ioj_35620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ioj_35620/08_2025/8ioj_35620.map" model { file = "/net/cci-nas-00/data/ceres_data/8ioj_35620/08_2025/8ioj_35620_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ioj_35620/08_2025/8ioj_35620_neut.cif" } resolution = 4.1 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= 0.001 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 150 5.16 5 C 22132 2.51 5 N 6122 2.21 5 O 6392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 269 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34796 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3257 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 393} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3217 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3245 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 392} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3229 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1562 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 12, 'TRANS': 184} Chain breaks: 6 Chain: "F" Number of atoms: 1216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1216 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain breaks: 1 Chain: "G" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1608 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 12, 'TRANS': 190} Chain: "H" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3257 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 393} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3217 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3245 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 392} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3229 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1133 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 138} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1124 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 140} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1133 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 138} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1124 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 140} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 7.28, per 1000 atoms: 0.21 Number of scatterers: 34796 At special positions: 0 Unit cell: (162.24, 170.56, 147.16, 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 150 16.00 O 6392 8.00 N 6122 7.00 C 22132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 189 " distance=2.04 Simple disulfide: pdb=" SG CYS I 169 " - pdb=" SG CYS I 189 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 8692 Ramachandran restraints generated. 4346 Oldfield, 0 Emsley, 4346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8158 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 40 sheets defined 45.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.554A pdb=" N ALA A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.510A pdb=" N LYS A 78 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 138 through 145 removed outlier: 3.948A pdb=" N THR A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.819A pdb=" N VAL A 154 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 192 removed outlier: 3.762A pdb=" N GLY A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.539A pdb=" N MET A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 4.370A pdb=" N ALA A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.937A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.509A pdb=" N GLU A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.065A pdb=" N GLU A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 433 through 442 removed outlier: 6.090A pdb=" N GLY A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 removed outlier: 4.145A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.950A pdb=" N ILE B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 210 through 228 Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.766A pdb=" N MET B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.905A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 348 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.720A pdb=" N LEU B 387 " --> pdb=" O HIS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 430 Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 150 through 159 removed outlier: 4.104A pdb=" N VAL C 154 " --> pdb=" O HIS C 150 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 155 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 192 Processing helix chain 'C' and resid 210 through 228 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 265 through 284 removed outlier: 6.083A pdb=" N PHE C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N THR C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.966A pdb=" N LEU C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 348 removed outlier: 3.846A pdb=" N MET C 346 " --> pdb=" O PHE C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 391 Processing helix chain 'C' and resid 410 through 418 Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 437 through 442 removed outlier: 4.057A pdb=" N ILE C 441 " --> pdb=" O GLU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 459 removed outlier: 4.300A pdb=" N TRP C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 57 Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 138 through 144 removed outlier: 3.892A pdb=" N THR D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.509A pdb=" N TYR D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 244 through 258 removed outlier: 3.776A pdb=" N GLY D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 285 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.988A pdb=" N ILE D 298 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.907A pdb=" N LEU D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 346 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 391 Processing helix chain 'D' and resid 409 through 422 removed outlier: 3.785A pdb=" N GLY D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 431 Processing helix chain 'D' and resid 433 through 442 removed outlier: 6.444A pdb=" N GLY D 439 " --> pdb=" O TYR D 435 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP D 440 " --> pdb=" O ARG D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 457 Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 97 through 110 Proline residue: E 103 - end of helix removed outlier: 4.146A pdb=" N SER E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 123 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.645A pdb=" N GLN E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 160 through 167 Processing helix chain 'E' and resid 173 through 185 Processing helix chain 'E' and resid 189 through 204 Proline residue: E 202 - end of helix Processing helix chain 'E' and resid 217 through 231 Processing helix chain 'E' and resid 237 through 244 Processing helix chain 'E' and resid 253 through 263 Processing helix chain 'F' and resid 84 through 87 removed outlier: 3.898A pdb=" N LYS F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 84 through 87' Processing helix chain 'F' and resid 88 through 93 removed outlier: 4.576A pdb=" N GLY F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 111 removed outlier: 3.781A pdb=" N ASP F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 123 removed outlier: 4.503A pdb=" N GLU F 120 " --> pdb=" O PRO F 116 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 144 Processing helix chain 'F' and resid 149 through 157 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.701A pdb=" N TYR F 164 " --> pdb=" O GLU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 185 removed outlier: 3.517A pdb=" N ARG F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 199 removed outlier: 4.308A pdb=" N ALA F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'G' and resid 83 through 94 Processing helix chain 'G' and resid 101 through 112 removed outlier: 3.609A pdb=" N GLY G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 149 through 154 Processing helix chain 'G' and resid 159 through 166 Processing helix chain 'G' and resid 170 through 185 removed outlier: 4.104A pdb=" N VAL G 175 " --> pdb=" O THR G 171 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA G 176 " --> pdb=" O THR G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 201 removed outlier: 3.539A pdb=" N ALA G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 233 removed outlier: 4.125A pdb=" N ASN G 233 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 248 Processing helix chain 'G' and resid 253 through 263 Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.553A pdb=" N ALA H 50 " --> pdb=" O PRO H 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER H 58 " --> pdb=" O ILE H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 78 removed outlier: 3.509A pdb=" N LYS H 78 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 110 through 119 Processing helix chain 'H' and resid 139 through 144 removed outlier: 4.486A pdb=" N THR H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 160 removed outlier: 3.819A pdb=" N VAL H 154 " --> pdb=" O HIS H 150 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU H 155 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 192 removed outlier: 3.762A pdb=" N GLY H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 230 Processing helix chain 'H' and resid 243 through 257 removed outlier: 3.539A pdb=" N MET H 247 " --> pdb=" O THR H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 285 removed outlier: 4.369A pdb=" N ALA H 273 " --> pdb=" O ALA H 269 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN H 274 " --> pdb=" O GLY H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 298 Processing helix chain 'H' and resid 307 through 319 removed outlier: 3.937A pdb=" N LEU H 311 " --> pdb=" O HIS H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 348 removed outlier: 3.508A pdb=" N GLU H 348 " --> pdb=" O ASP H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 391 removed outlier: 4.066A pdb=" N GLU H 389 " --> pdb=" O PRO H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 422 Processing helix chain 'H' and resid 424 through 431 Processing helix chain 'H' and resid 433 through 442 removed outlier: 6.090A pdb=" N GLY H 439 " --> pdb=" O TYR H 435 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP H 440 " --> pdb=" O ARG H 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 460 removed outlier: 4.146A pdb=" N LEU H 456 " --> pdb=" O LEU H 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 58 Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'I' and resid 109 through 118 removed outlier: 3.950A pdb=" N ILE I 113 " --> pdb=" O SER I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 143 Processing helix chain 'I' and resid 151 through 160 Processing helix chain 'I' and resid 178 through 192 Processing helix chain 'I' and resid 210 through 228 Processing helix chain 'I' and resid 243 through 258 removed outlier: 3.765A pdb=" N MET I 247 " --> pdb=" O THR I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 270 Processing helix chain 'I' and resid 270 through 285 Processing helix chain 'I' and resid 294 through 298 Processing helix chain 'I' and resid 307 through 319 removed outlier: 3.905A pdb=" N LEU I 311 " --> pdb=" O HIS I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 348 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 391 removed outlier: 3.721A pdb=" N LEU I 387 " --> pdb=" O HIS I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 430 Processing helix chain 'I' and resid 433 through 438 Processing helix chain 'I' and resid 448 through 453 Processing helix chain 'J' and resid 46 through 58 Processing helix chain 'J' and resid 101 through 105 Processing helix chain 'J' and resid 109 through 118 Processing helix chain 'J' and resid 150 through 159 removed outlier: 4.105A pdb=" N VAL J 154 " --> pdb=" O HIS J 150 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU J 155 " --> pdb=" O GLY J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 192 Processing helix chain 'J' and resid 210 through 228 Processing helix chain 'J' and resid 243 through 257 Processing helix chain 'J' and resid 265 through 284 removed outlier: 6.082A pdb=" N PHE J 271 " --> pdb=" O LEU J 267 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N THR J 272 " --> pdb=" O THR J 268 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA J 273 " --> pdb=" O ALA J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 298 Processing helix chain 'J' and resid 307 through 319 removed outlier: 3.966A pdb=" N LEU J 311 " --> pdb=" O HIS J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 348 removed outlier: 3.847A pdb=" N MET J 346 " --> pdb=" O PHE J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 391 Processing helix chain 'J' and resid 410 through 419 Processing helix chain 'J' and resid 423 through 431 Processing helix chain 'J' and resid 437 through 442 removed outlier: 4.057A pdb=" N ILE J 441 " --> pdb=" O GLU J 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 459 removed outlier: 4.300A pdb=" N TRP J 459 " --> pdb=" O ALA J 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 57 Processing helix chain 'K' and resid 101 through 105 Processing helix chain 'K' and resid 110 through 119 Processing helix chain 'K' and resid 138 through 145 removed outlier: 3.664A pdb=" N PHE K 145 " --> pdb=" O LEU K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 160 Processing helix chain 'K' and resid 178 through 192 removed outlier: 3.509A pdb=" N TYR K 182 " --> pdb=" O SER K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 230 Processing helix chain 'K' and resid 244 through 258 removed outlier: 3.776A pdb=" N GLY K 258 " --> pdb=" O ALA K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 285 Processing helix chain 'K' and resid 294 through 299 removed outlier: 3.989A pdb=" N ILE K 298 " --> pdb=" O MET K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 319 removed outlier: 3.906A pdb=" N LEU K 311 " --> pdb=" O HIS K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 346 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 391 Processing helix chain 'K' and resid 409 through 422 removed outlier: 3.785A pdb=" N GLY K 413 " --> pdb=" O GLY K 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 424 through 431 Processing helix chain 'K' and resid 433 through 442 removed outlier: 6.444A pdb=" N GLY K 439 " --> pdb=" O TYR K 435 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP K 440 " --> pdb=" O ARG K 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 457 Processing helix chain 'L' and resid 315 through 322 removed outlier: 3.653A pdb=" N ILE L 319 " --> pdb=" O GLY L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 357 removed outlier: 4.218A pdb=" N GLY L 357 " --> pdb=" O VAL L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 418 Processing helix chain 'M' and resid 315 through 322 removed outlier: 3.603A pdb=" N ILE M 319 " --> pdb=" O GLY M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 357 removed outlier: 3.552A pdb=" N ILE M 356 " --> pdb=" O PRO M 352 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY M 357 " --> pdb=" O VAL M 353 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 372 removed outlier: 4.262A pdb=" N VAL M 371 " --> pdb=" O ASP M 367 " (cutoff:3.500A) Processing helix chain 'M' and resid 388 through 390 No H-bonds generated for 'chain 'M' and resid 388 through 390' Processing helix chain 'M' and resid 412 through 418 Processing helix chain 'N' and resid 315 through 322 removed outlier: 3.654A pdb=" N ILE N 319 " --> pdb=" O GLY N 315 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 357 removed outlier: 4.217A pdb=" N GLY N 357 " --> pdb=" O VAL N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 412 through 418 Processing helix chain 'O' and resid 315 through 322 removed outlier: 3.604A pdb=" N ILE O 319 " --> pdb=" O GLY O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 350 through 357 removed outlier: 3.553A pdb=" N ILE O 356 " --> pdb=" O PRO O 352 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY O 357 " --> pdb=" O VAL O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 367 through 372 removed outlier: 4.261A pdb=" N VAL O 371 " --> pdb=" O ASP O 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 388 through 390 No H-bonds generated for 'chain 'O' and resid 388 through 390' Processing helix chain 'O' and resid 412 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 86 removed outlier: 6.126A pdb=" N CYS A 81 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 99 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG A 38 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU A 132 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N SER A 40 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU A 130 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 235 removed outlier: 6.705A pdb=" N LEU A 167 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYS A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS A 169 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET A 166 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 265 removed outlier: 6.137A pdb=" N ILE A 262 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N HIS A 291 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N HIS A 264 " --> pdb=" O HIS A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 86 removed outlier: 6.322A pdb=" N PHE B 97 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 84 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE B 95 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 36 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 234 through 236 removed outlier: 7.625A pdb=" N THR B 197 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N MET B 166 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE B 399 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY B 168 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 263 removed outlier: 5.870A pdb=" N ILE B 262 " --> pdb=" O HIS B 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 324 removed outlier: 5.974A pdb=" N LEU B 323 " --> pdb=" O VAL B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 86 removed outlier: 6.525A pdb=" N PHE C 97 " --> pdb=" O TYR C 82 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 84 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE C 95 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 34 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE C 135 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 36 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 305 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 196 through 198 removed outlier: 7.520A pdb=" N GLN C 398 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA C 375 " --> pdb=" O GLN C 398 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU C 323 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AB3, first strand: chain 'D' and resid 80 through 86 removed outlier: 5.655A pdb=" N CYS D 81 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA D 99 " --> pdb=" O CYS D 81 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU D 34 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE D 135 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA D 36 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.753A pdb=" N LEU D 167 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LYS D 198 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N CYS D 169 " --> pdb=" O LYS D 198 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET D 166 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN D 398 " --> pdb=" O PRO D 373 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA D 375 " --> pdb=" O GLN D 398 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 261 through 265 removed outlier: 3.695A pdb=" N HIS D 291 " --> pdb=" O HIS D 264 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 350 through 351 Processing sheet with id=AB7, first strand: chain 'H' and resid 80 through 86 removed outlier: 6.125A pdb=" N CYS H 81 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA H 99 " --> pdb=" O CYS H 81 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG H 38 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU H 132 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N SER H 40 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU H 130 " --> pdb=" O SER H 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 234 through 235 removed outlier: 6.704A pdb=" N LEU H 167 " --> pdb=" O PHE H 196 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYS H 198 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N CYS H 169 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET H 166 " --> pdb=" O LEU H 397 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 261 through 265 removed outlier: 6.137A pdb=" N ILE H 262 " --> pdb=" O HIS H 289 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N HIS H 291 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N HIS H 264 " --> pdb=" O HIS H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H' and resid 350 through 351 Processing sheet with id=AC2, first strand: chain 'I' and resid 80 through 86 removed outlier: 6.322A pdb=" N PHE I 97 " --> pdb=" O TYR I 82 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE I 84 " --> pdb=" O PHE I 95 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE I 95 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA I 36 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 234 through 236 removed outlier: 7.624A pdb=" N THR I 197 " --> pdb=" O TYR I 236 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N MET I 166 " --> pdb=" O LEU I 397 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE I 399 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY I 168 " --> pdb=" O PHE I 399 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 261 through 263 removed outlier: 5.870A pdb=" N ILE I 262 " --> pdb=" O HIS I 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 322 through 324 removed outlier: 5.974A pdb=" N LEU I 323 " --> pdb=" O VAL I 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'J' and resid 80 through 86 removed outlier: 6.526A pdb=" N PHE J 97 " --> pdb=" O TYR J 82 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE J 84 " --> pdb=" O PHE J 95 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE J 95 " --> pdb=" O ILE J 84 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU J 34 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE J 135 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA J 36 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY J 305 " --> pdb=" O LEU J 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 196 through 198 removed outlier: 7.520A pdb=" N GLN J 398 " --> pdb=" O PRO J 373 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA J 375 " --> pdb=" O GLN J 398 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU J 323 " --> pdb=" O VAL J 374 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 263 through 264 Processing sheet with id=AC9, first strand: chain 'K' and resid 80 through 86 removed outlier: 5.655A pdb=" N CYS K 81 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA K 99 " --> pdb=" O CYS K 81 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU K 34 " --> pdb=" O ILE K 135 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE K 135 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA K 36 " --> pdb=" O GLU K 133 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 234 through 235 removed outlier: 6.752A pdb=" N LEU K 167 " --> pdb=" O PHE K 196 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LYS K 198 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N CYS K 169 " --> pdb=" O LYS K 198 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET K 166 " --> pdb=" O LEU K 397 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN K 398 " --> pdb=" O PRO K 373 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA K 375 " --> pdb=" O GLN K 398 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 261 through 265 removed outlier: 3.694A pdb=" N HIS K 291 " --> pdb=" O HIS K 264 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 350 through 351 Processing sheet with id=AD4, first strand: chain 'L' and resid 344 through 345 removed outlier: 3.721A pdb=" N GLY L 425 " --> pdb=" O LEU L 400 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR L 398 " --> pdb=" O VAL L 427 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 326 through 328 Processing sheet with id=AD6, first strand: chain 'M' and resid 290 through 292 removed outlier: 3.685A pdb=" N ARG M 432 " --> pdb=" O VAL M 291 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL M 427 " --> pdb=" O ASP M 386 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP M 386 " --> pdb=" O VAL M 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU M 429 " --> pdb=" O VAL M 384 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY M 360 " --> pdb=" O VAL M 306 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 290 through 292 removed outlier: 3.685A pdb=" N ARG M 432 " --> pdb=" O VAL M 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY M 425 " --> pdb=" O LEU M 400 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR M 398 " --> pdb=" O VAL M 427 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 326 through 328 Processing sheet with id=AD9, first strand: chain 'N' and resid 344 through 345 removed outlier: 3.721A pdb=" N GLY N 425 " --> pdb=" O LEU N 400 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TYR N 398 " --> pdb=" O VAL N 427 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 326 through 328 Processing sheet with id=AE2, first strand: chain 'O' and resid 290 through 292 removed outlier: 3.685A pdb=" N ARG O 432 " --> pdb=" O VAL O 291 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL O 427 " --> pdb=" O ASP O 386 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP O 386 " --> pdb=" O VAL O 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU O 429 " --> pdb=" O VAL O 384 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY O 360 " --> pdb=" O VAL O 306 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 290 through 292 removed outlier: 3.685A pdb=" N ARG O 432 " --> pdb=" O VAL O 291 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY O 425 " --> pdb=" O LEU O 400 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR O 398 " --> pdb=" O VAL O 427 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 326 through 328 1459 hydrogen bonds defined for protein. 4152 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: 6.06 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.52: 26155 1.52 - 1.85: 9444 1.85 - 2.18: 0 2.18 - 2.52: 0 2.52 - 2.85: 2 Bond restraints: 35601 Sorted by residual: bond pdb=" C ASP L 367 " pdb=" N ARG L 369 " ideal model delta sigma weight residual 1.329 2.848 -1.519 1.40e-02 5.10e+03 1.18e+04 bond pdb=" C ASP N 367 " pdb=" N ARG N 369 " ideal model delta sigma weight residual 1.329 2.848 -1.519 1.40e-02 5.10e+03 1.18e+04 bond pdb=" CA PRO L 433 " pdb=" C PRO L 433 " ideal model delta sigma weight residual 1.517 1.575 -0.058 9.30e-03 1.16e+04 3.86e+01 bond pdb=" CA PRO N 433 " pdb=" C PRO N 433 " ideal model delta sigma weight residual 1.517 1.574 -0.057 9.30e-03 1.16e+04 3.78e+01 bond pdb=" N VAL N 430 " pdb=" CA VAL N 430 " ideal model delta sigma weight residual 1.456 1.511 -0.056 1.11e-02 8.12e+03 2.51e+01 ... (remaining 35596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.61: 48065 5.61 - 11.22: 130 11.22 - 16.83: 23 16.83 - 22.44: 4 22.44 - 28.05: 2 Bond angle restraints: 48224 Sorted by residual: angle pdb=" N VAL L 431 " pdb=" CA VAL L 431 " pdb=" C VAL L 431 " ideal model delta sigma weight residual 110.74 138.79 -28.05 9.10e-01 1.21e+00 9.50e+02 angle pdb=" N VAL N 431 " pdb=" CA VAL N 431 " pdb=" C VAL N 431 " ideal model delta sigma weight residual 110.74 138.77 -28.03 9.10e-01 1.21e+00 9.49e+02 angle pdb=" O ASP N 367 " pdb=" C ASP N 367 " pdb=" N ARG N 369 " ideal model delta sigma weight residual 121.74 107.24 14.50 1.31e+00 5.83e-01 1.23e+02 angle pdb=" O ASP L 367 " pdb=" C ASP L 367 " pdb=" N ARG L 369 " ideal model delta sigma weight residual 121.74 107.26 14.48 1.31e+00 5.83e-01 1.22e+02 angle pdb=" N PRO N 433 " pdb=" CA PRO N 433 " pdb=" C PRO N 433 " ideal model delta sigma weight residual 110.70 123.72 -13.02 1.22e+00 6.72e-01 1.14e+02 ... (remaining 48219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 18550 17.96 - 35.91: 1931 35.91 - 53.87: 504 53.87 - 71.82: 145 71.82 - 89.78: 23 Dihedral angle restraints: 21153 sinusoidal: 8467 harmonic: 12686 Sorted by residual: dihedral pdb=" N ALA N 301 " pdb=" C ALA N 301 " pdb=" CA ALA N 301 " pdb=" CB ALA N 301 " ideal model delta harmonic sigma weight residual 122.90 154.15 -31.25 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" N ALA L 301 " pdb=" C ALA L 301 " pdb=" CA ALA L 301 " pdb=" CB ALA L 301 " ideal model delta harmonic sigma weight residual 122.90 154.14 -31.24 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" C ALA L 301 " pdb=" N ALA L 301 " pdb=" CA ALA L 301 " pdb=" CB ALA L 301 " ideal model delta harmonic sigma weight residual -122.60 -153.76 31.16 0 2.50e+00 1.60e-01 1.55e+02 ... (remaining 21150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 5201 0.281 - 0.562: 25 0.562 - 0.843: 5 0.843 - 1.124: 0 1.124 - 1.405: 2 Chirality restraints: 5233 Sorted by residual: chirality pdb=" CA ALA N 301 " pdb=" N ALA N 301 " pdb=" C ALA N 301 " pdb=" CB ALA N 301 " both_signs ideal model delta sigma weight residual False 2.48 1.08 1.41 2.00e-01 2.50e+01 4.94e+01 chirality pdb=" CA ALA L 301 " pdb=" N ALA L 301 " pdb=" C ALA L 301 " pdb=" CB ALA L 301 " both_signs ideal model delta sigma weight residual False 2.48 1.08 1.40 2.00e-01 2.50e+01 4.92e+01 chirality pdb=" CA LYS M 377 " pdb=" N LYS M 377 " pdb=" C LYS M 377 " pdb=" CB LYS M 377 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 5230 not shown) Planarity restraints: 6307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP N 367 " -0.116 2.00e-02 2.50e+03 1.80e-01 3.25e+02 pdb=" C ASP N 367 " 0.306 2.00e-02 2.50e+03 pdb=" O ASP N 367 " -0.144 2.00e-02 2.50e+03 pdb=" N ARG N 369 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 367 " 0.116 2.00e-02 2.50e+03 1.80e-01 3.24e+02 pdb=" C ASP L 367 " -0.306 2.00e-02 2.50e+03 pdb=" O ASP L 367 " 0.143 2.00e-02 2.50e+03 pdb=" N ARG L 369 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE O 326 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ILE O 326 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE O 326 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE O 327 " 0.019 2.00e-02 2.50e+03 ... (remaining 6304 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 361 2.50 - 3.10: 27878 3.10 - 3.70: 54303 3.70 - 4.30: 76253 4.30 - 4.90: 123706 Nonbonded interactions: 282501 Sorted by model distance: nonbonded pdb=" OG SER A 367 " pdb=" OD2 ASP K 103 " model vdw 1.901 3.040 nonbonded pdb=" OG SER J 129 " pdb=" O ASN J 303 " model vdw 2.089 3.040 nonbonded pdb=" OG SER C 129 " pdb=" O ASN C 303 " model vdw 2.089 3.040 nonbonded pdb=" NZ LYS C 336 " pdb=" OH TYR C 435 " model vdw 2.155 3.120 nonbonded pdb=" NZ LYS J 336 " pdb=" OH TYR J 435 " model vdw 2.156 3.120 ... (remaining 282496 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 59 or resid 76 through 173 or resid 177 through \ 399 or resid 406 through 458)) selection = (chain 'B' and (resid 21 through 328 or resid 335 through 399 or resid 406 throu \ gh 458)) selection = (chain 'C' and (resid 21 through 59 or resid 76 through 173 or resid 175 or resi \ d 178 through 328 or resid 335 through 399 or resid 406 through 458)) selection = (chain 'D' and (resid 21 through 59 or resid 76 through 328 or resid 335 through \ 458)) selection = (chain 'H' and (resid 21 through 59 or resid 76 through 173 or resid 177 through \ 399 or resid 406 through 458)) selection = (chain 'I' and (resid 21 through 328 or resid 335 through 399 or resid 406 throu \ gh 458)) selection = (chain 'J' and (resid 21 through 59 or resid 76 through 173 or resid 175 or resi \ d 178 through 328 or resid 335 through 399 or resid 406 through 458)) selection = (chain 'K' and (resid 21 through 59 or resid 76 through 328 or resid 335 through \ 458)) } ncs_group { reference = chain 'E' selection = (chain 'G' and (resid 62 through 152 or resid 154 through 186 or resid 188 throu \ gh 206 or resid 208 through 210 or resid 212 through 244 or resid 246 through 24 \ 7 or resid 249 through 264)) } ncs_group { reference = (chain 'L' and (resid 288 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB )) or resid 295 through 357 or (resid 358 and (name N \ or name CA or name C or name O or name CB )) or resid 359 through 369 or (resid \ 370 and (name N or name CA or name C or name O or name CB )) or resid 371 throug \ h 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) or \ resid 409 through 418 or (resid 419 and (name N or name CA or name C or name O o \ r name CB )) or resid 420 through 435 or (resid 436 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'M' and (resid 288 through 316 or (resid 317 and (name N or name CA or na \ me C or name O or name CB )) or resid 318 through 367 or (resid 369 through 370 \ and (name N or name CA or name C or name O or name CB )) or resid 371 through 43 \ 6)) selection = (chain 'N' and (resid 288 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB )) or resid 295 through 357 or (resid 358 and (name N \ or name CA or name C or name O or name CB )) or resid 359 through 369 or (resid \ 370 and (name N or name CA or name C or name O or name CB )) or resid 371 throug \ h 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) or \ resid 409 through 418 or (resid 419 and (name N or name CA or name C or name O o \ r name CB )) or resid 420 through 435 or (resid 436 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'O' and (resid 288 through 316 or (resid 317 and (name N or name CA or na \ me C or name O or name CB )) or resid 318 through 367 or (resid 369 through 370 \ and (name N or name CA or name C or name O or name CB )) or resid 371 through 43 \ 6)) } 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 group one per residue 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: 5.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 27.990 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 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 : 0.014 1.519 35604 Z= 0.911 Angle : 1.039 28.045 48228 Z= 0.654 Chirality : 0.070 1.405 5233 Planarity : 0.007 0.180 6307 Dihedral : 16.281 89.778 12989 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.93 % Favored : 88.86 % Rotamer: Outliers : 6.13 % Allowed : 10.44 % Favored : 83.43 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.72 (0.11), residues: 4346 helix: -1.85 (0.11), residues: 1712 sheet: -2.38 (0.18), residues: 626 loop : -3.03 (0.12), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 316 TYR 0.015 0.002 TYR J 182 PHE 0.024 0.002 PHE I 266 TRP 0.015 0.002 TRP J 382 HIS 0.007 0.001 HIS H 291 Details of bonding type rmsd covalent geometry : bond 0.01367 (35601) covalent geometry : angle 1.03873 (48224) SS BOND : bond 0.00469 ( 2) SS BOND : angle 2.92134 ( 4) hydrogen bonds : bond 0.16011 ( 1457) hydrogen bonds : angle 7.22795 ( 4152) Misc. bond : bond 0.21501 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8692 Ramachandran restraints generated. 4346 Oldfield, 0 Emsley, 4346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8692 Ramachandran restraints generated. 4346 Oldfield, 0 Emsley, 4346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 1046 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.8261 (p0) cc_final: 0.7438 (t0) REVERT: A 42 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8033 (tp40) REVERT: A 49 GLU cc_start: 0.7339 (tp30) cc_final: 0.6749 (tp30) REVERT: A 112 ASN cc_start: 0.7318 (t0) cc_final: 0.6989 (t0) REVERT: A 125 LYS cc_start: 0.7425 (pttt) cc_final: 0.7118 (tttt) REVERT: A 146 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7723 (tp40) REVERT: A 161 LYS cc_start: 0.7844 (mmtp) cc_final: 0.7506 (mmtt) REVERT: A 216 LEU cc_start: 0.8694 (mt) cc_final: 0.8472 (mt) REVERT: A 220 ASP cc_start: 0.7994 (t0) cc_final: 0.7610 (m-30) REVERT: A 283 ASP cc_start: 0.6869 (m-30) cc_final: 0.6380 (m-30) REVERT: A 304 HIS cc_start: 0.8358 (t-90) cc_final: 0.8111 (t-90) REVERT: A 315 LEU cc_start: 0.9210 (tt) cc_final: 0.8933 (tt) REVERT: A 426 GLN cc_start: 0.8131 (tt0) cc_final: 0.7682 (tt0) REVERT: A 452 LEU cc_start: 0.5825 (pt) cc_final: 0.5498 (tp) REVERT: B 103 ASP cc_start: 0.8111 (m-30) cc_final: 0.7580 (m-30) REVERT: B 122 PHE cc_start: 0.9019 (m-80) cc_final: 0.8691 (m-80) REVERT: B 172 LYS cc_start: 0.6360 (tttt) cc_final: 0.6024 (mmtt) REVERT: B 203 ILE cc_start: 0.7734 (mt) cc_final: 0.6987 (tt) REVERT: B 209 GLN cc_start: 0.8105 (mt0) cc_final: 0.7844 (mt0) REVERT: B 210 ARG cc_start: 0.5983 (mmt-90) cc_final: 0.5384 (mmt180) REVERT: B 224 LYS cc_start: 0.7570 (tttt) cc_final: 0.6946 (tttt) REVERT: B 231 GLU cc_start: 0.7251 (tt0) cc_final: 0.6942 (tt0) REVERT: B 261 ILE cc_start: 0.9109 (pt) cc_final: 0.8868 (tt) REVERT: B 302 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7309 (tpp80) REVERT: B 328 VAL cc_start: 0.7569 (t) cc_final: 0.7269 (p) REVERT: B 336 LYS cc_start: 0.5728 (pttt) cc_final: 0.5159 (ttpt) REVERT: B 350 HIS cc_start: 0.8074 (t-90) cc_final: 0.7786 (t-90) REVERT: B 390 ILE cc_start: 0.8726 (mm) cc_final: 0.8436 (pt) REVERT: B 417 ASN cc_start: 0.6362 (m110) cc_final: 0.5875 (m110) REVERT: C 90 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.6067 (tm-30) REVERT: C 120 ASN cc_start: 0.8618 (p0) cc_final: 0.8371 (p0) REVERT: C 128 ARG cc_start: 0.7066 (tpp80) cc_final: 0.6540 (ttt-90) REVERT: C 202 ASN cc_start: 0.7521 (p0) cc_final: 0.7279 (p0) REVERT: C 248 MET cc_start: 0.8763 (mmp) cc_final: 0.8546 (tpp) REVERT: C 390 ILE cc_start: 0.8726 (mm) cc_final: 0.8457 (mm) REVERT: C 428 ARG cc_start: 0.8890 (ttp-170) cc_final: 0.8588 (ttt-90) REVERT: C 432 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7133 (mtp85) REVERT: D 76 ARG cc_start: 0.6671 (ptt180) cc_final: 0.6234 (mtp180) REVERT: D 95 PHE cc_start: 0.7862 (m-80) cc_final: 0.7399 (m-80) REVERT: D 125 LYS cc_start: 0.6633 (pttt) cc_final: 0.5893 (tppt) REVERT: D 127 ILE cc_start: 0.8235 (mm) cc_final: 0.7990 (mt) REVERT: D 171 ILE cc_start: 0.8843 (tp) cc_final: 0.8579 (tt) REVERT: D 203 ILE cc_start: 0.6507 (mm) cc_final: 0.5837 (mm) REVERT: D 206 GLN cc_start: 0.6987 (mt0) cc_final: 0.6692 (mp10) REVERT: D 208 PHE cc_start: 0.7551 (p90) cc_final: 0.7050 (p90) REVERT: D 231 GLU cc_start: 0.6482 (mt-10) cc_final: 0.6249 (mm-30) REVERT: D 344 ASP cc_start: 0.8458 (m-30) cc_final: 0.8065 (t0) REVERT: D 357 ARG cc_start: 0.7371 (mtp85) cc_final: 0.6900 (mtp85) REVERT: D 359 VAL cc_start: 0.9239 (t) cc_final: 0.9033 (m) REVERT: D 363 GLN cc_start: 0.8224 (tp40) cc_final: 0.7668 (tm-30) REVERT: D 435 TYR cc_start: 0.6799 (t80) cc_final: 0.6471 (t80) REVERT: E 82 LEU cc_start: 0.6440 (mp) cc_final: 0.6176 (mm) REVERT: E 89 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8114 (mt-10) REVERT: E 119 GLU cc_start: 0.6514 (tt0) cc_final: 0.6100 (tt0) REVERT: E 164 TYR cc_start: 0.7130 (t80) cc_final: 0.6815 (t80) REVERT: E 171 THR cc_start: 0.8981 (t) cc_final: 0.8712 (m) REVERT: E 173 GLN cc_start: 0.7065 (mt0) cc_final: 0.6854 (tt0) REVERT: E 184 ARG cc_start: 0.6878 (mpt180) cc_final: 0.4732 (ttp80) REVERT: E 205 ARG cc_start: 0.7291 (mmt-90) cc_final: 0.6996 (mtp85) REVERT: E 226 TYR cc_start: 0.6904 (m-10) cc_final: 0.6530 (m-80) REVERT: E 228 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.5417 (mmm160) REVERT: F 69 ARG cc_start: 0.4947 (OUTLIER) cc_final: 0.4390 (mtm180) REVERT: F 95 MET cc_start: 0.4844 (pmm) cc_final: 0.4303 (mpp) REVERT: G 117 THR cc_start: 0.7144 (p) cc_final: 0.6859 (t) REVERT: G 173 GLN cc_start: 0.7231 (mt0) cc_final: 0.6780 (mt0) REVERT: G 185 ASN cc_start: 0.7270 (t0) cc_final: 0.7035 (p0) REVERT: G 201 TYR cc_start: 0.6696 (t80) cc_final: 0.6032 (t80) REVERT: G 210 TRP cc_start: 0.6141 (t-100) cc_final: 0.5472 (t-100) REVERT: H 144 THR cc_start: 0.6279 (OUTLIER) cc_final: 0.5869 (t) REVERT: H 157 ASP cc_start: 0.7603 (m-30) cc_final: 0.6672 (m-30) REVERT: H 252 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7152 (mm-30) REVERT: H 339 THR cc_start: 0.8221 (m) cc_final: 0.7637 (t) REVERT: H 442 LEU cc_start: 0.5532 (OUTLIER) cc_final: 0.5268 (tp) REVERT: I 57 GLU cc_start: 0.5283 (tp30) cc_final: 0.4668 (tp30) REVERT: I 78 LYS cc_start: 0.6547 (pttp) cc_final: 0.5839 (mttm) REVERT: I 127 ILE cc_start: 0.7877 (mm) cc_final: 0.7305 (tp) REVERT: I 202 ASN cc_start: 0.7716 (p0) cc_final: 0.7003 (p0) REVERT: I 302 ARG cc_start: 0.6418 (ttm-80) cc_final: 0.6157 (tmm160) REVERT: I 307 HIS cc_start: 0.8591 (t-90) cc_final: 0.7998 (t-90) REVERT: I 315 LEU cc_start: 0.8550 (tt) cc_final: 0.7820 (tt) REVERT: I 336 LYS cc_start: 0.5070 (pttt) cc_final: 0.4277 (ptpp) REVERT: I 380 HIS cc_start: 0.6309 (p90) cc_final: 0.5737 (p90) REVERT: I 412 PRO cc_start: 0.7644 (Cg_exo) cc_final: 0.7341 (Cg_endo) REVERT: J 29 LYS cc_start: 0.5913 (mttt) cc_final: 0.5352 (ttpt) REVERT: J 83 HIS cc_start: 0.8230 (t-90) cc_final: 0.7813 (t-170) REVERT: J 94 TYR cc_start: 0.7446 (m-80) cc_final: 0.6966 (m-80) REVERT: J 95 PHE cc_start: 0.6966 (m-10) cc_final: 0.6383 (m-10) REVERT: J 107 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6790 (tt0) REVERT: J 210 ARG cc_start: 0.6617 (mmt180) cc_final: 0.6343 (mmt180) REVERT: J 224 LYS cc_start: 0.6421 (ttpt) cc_final: 0.6190 (mmmt) REVERT: J 255 LYS cc_start: 0.8598 (tmtt) cc_final: 0.8326 (tppt) REVERT: J 371 VAL cc_start: 0.8109 (m) cc_final: 0.7897 (m) REVERT: K 22 TYR cc_start: 0.6277 (t80) cc_final: 0.5957 (t80) REVERT: K 169 CYS cc_start: 0.7344 (t) cc_final: 0.6968 (p) REVERT: K 194 LEU cc_start: 0.7367 (mt) cc_final: 0.6864 (mt) REVERT: K 195 ASP cc_start: 0.7294 (m-30) cc_final: 0.7047 (m-30) REVERT: K 203 ILE cc_start: 0.6095 (mm) cc_final: 0.5838 (mt) REVERT: K 206 GLN cc_start: 0.7455 (mt0) cc_final: 0.6891 (mp10) REVERT: K 222 ILE cc_start: 0.8612 (mt) cc_final: 0.8198 (mm) REVERT: K 224 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7456 (tppt) REVERT: K 279 LYS cc_start: 0.7472 (mmmt) cc_final: 0.6924 (mtpt) REVERT: K 303 ASN cc_start: 0.7851 (m-40) cc_final: 0.7526 (m-40) REVERT: K 324 HIS cc_start: 0.7559 (m170) cc_final: 0.7044 (m-70) REVERT: K 328 VAL cc_start: 0.7750 (t) cc_final: 0.7318 (m) REVERT: L 431 VAL cc_start: 0.0156 (OUTLIER) cc_final: -0.0445 (m) REVERT: M 316 GLU cc_start: 0.3976 (OUTLIER) cc_final: 0.2984 (tt0) REVERT: M 342 LYS cc_start: 0.1205 (OUTLIER) cc_final: 0.0588 (mmtm) REVERT: M 343 ARG cc_start: 0.0957 (OUTLIER) cc_final: -0.0220 (mmm160) REVERT: N 292 ARG cc_start: -0.0231 (OUTLIER) cc_final: -0.0623 (ttp-110) REVERT: N 361 VAL cc_start: 0.4082 (OUTLIER) cc_final: 0.3654 (p) REVERT: N 379 GLU cc_start: -0.1404 (OUTLIER) cc_final: -0.2185 (mp0) REVERT: N 396 ASP cc_start: 0.3731 (OUTLIER) cc_final: 0.2875 (m-30) REVERT: N 402 VAL cc_start: -0.1784 (OUTLIER) cc_final: -0.2012 (p) REVERT: N 413 SER cc_start: 0.2787 (OUTLIER) cc_final: 0.2479 (t) REVERT: O 341 TRP cc_start: 0.2457 (t-100) cc_final: 0.1343 (t-100) REVERT: O 342 LYS cc_start: 0.4020 (OUTLIER) cc_final: 0.2940 (tptp) REVERT: O 426 MET cc_start: -0.1096 (ttt) cc_final: -0.1336 (tmm) outliers start: 222 outliers final: 46 residues processed: 1239 average time/residue: 0.2113 time to fit residues: 407.6731 Evaluate side-chains 675 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 614 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 HIS B 284 ASN B 301 GLN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 HIS B 383 HIS B 398 GLN B 417 ASN C 112 ASN C 209 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 181 ASN ** D 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 GLN E 130 ASN E 233 ASN G 144 GLN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN H 42 GLN H 112 ASN H 153 GLN ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 380 HIS ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 ASN ** I 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 HIS I 398 GLN I 417 ASN J 112 ASN ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 GLN K 284 ASN K 291 HIS ** K 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 324 HIS K 380 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.154730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119267 restraints weight = 61771.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119152 restraints weight = 60782.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120926 restraints weight = 40294.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120307 restraints weight = 27796.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120448 restraints weight = 27567.351| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35604 Z= 0.187 Angle : 0.714 14.468 48228 Z= 0.373 Chirality : 0.047 0.231 5233 Planarity : 0.006 0.100 6307 Dihedral : 5.611 38.792 4819 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.15 % Favored : 92.74 % Rotamer: Outliers : 0.17 % Allowed : 5.55 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.12), residues: 4350 helix: -0.40 (0.12), residues: 1731 sheet: -1.82 (0.18), residues: 616 loop : -2.45 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 366 TYR 0.020 0.002 TYR I 236 PHE 0.042 0.002 PHE O 332 TRP 0.026 0.002 TRP K 365 HIS 0.012 0.001 HIS J 380 Details of bonding type rmsd covalent geometry : bond 0.00423 (35601) covalent geometry : angle 0.71425 (48224) SS BOND : bond 0.00322 ( 2) SS BOND : angle 2.02539 ( 4) hydrogen bonds : bond 0.04371 ( 1457) hydrogen bonds : angle 5.38104 ( 4152) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 785 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7548 (p0) cc_final: 0.7009 (t0) REVERT: A 49 GLU cc_start: 0.6186 (tp30) cc_final: 0.5934 (tp30) REVERT: A 125 LYS cc_start: 0.7242 (pttt) cc_final: 0.6576 (ptpt) REVERT: A 172 LYS cc_start: 0.6409 (tptm) cc_final: 0.4839 (ptpt) REVERT: A 279 LYS cc_start: 0.7398 (tptp) cc_final: 0.6621 (mmtt) REVERT: A 283 ASP cc_start: 0.7043 (m-30) cc_final: 0.6769 (m-30) REVERT: A 299 ASP cc_start: 0.7723 (p0) cc_final: 0.7477 (p0) REVERT: A 301 GLN cc_start: 0.8136 (tp40) cc_final: 0.7778 (tp40) REVERT: A 315 LEU cc_start: 0.9016 (tt) cc_final: 0.8680 (tt) REVERT: B 103 ASP cc_start: 0.7742 (m-30) cc_final: 0.7301 (m-30) REVERT: B 122 PHE cc_start: 0.8630 (m-80) cc_final: 0.8263 (m-80) REVERT: B 162 TYR cc_start: 0.8525 (m-80) cc_final: 0.7969 (m-80) REVERT: B 177 LEU cc_start: 0.7960 (mp) cc_final: 0.7757 (mp) REVERT: B 203 ILE cc_start: 0.7752 (mt) cc_final: 0.7133 (tt) REVERT: B 224 LYS cc_start: 0.7932 (tttt) cc_final: 0.7599 (mmtm) REVERT: B 261 ILE cc_start: 0.9238 (pt) cc_final: 0.8918 (tt) REVERT: B 302 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.7156 (tpp80) REVERT: B 336 LYS cc_start: 0.6333 (pttt) cc_final: 0.5400 (ttpt) REVERT: B 350 HIS cc_start: 0.7731 (t-90) cc_final: 0.7432 (t-90) REVERT: B 372 LEU cc_start: 0.8908 (mt) cc_final: 0.8495 (mt) REVERT: B 385 PRO cc_start: 0.9056 (Cg_endo) cc_final: 0.8724 (Cg_exo) REVERT: C 48 ASP cc_start: 0.7755 (m-30) cc_final: 0.7445 (m-30) REVERT: C 120 ASN cc_start: 0.8171 (p0) cc_final: 0.7908 (p0) REVERT: C 128 ARG cc_start: 0.6837 (tpp80) cc_final: 0.6530 (ttt-90) REVERT: C 155 GLU cc_start: 0.8322 (pp20) cc_final: 0.8096 (pp20) REVERT: C 202 ASN cc_start: 0.7397 (p0) cc_final: 0.7121 (p0) REVERT: C 336 LYS cc_start: 0.6430 (mttt) cc_final: 0.5439 (mtmm) REVERT: D 94 TYR cc_start: 0.7928 (m-80) cc_final: 0.7683 (m-10) REVERT: D 125 LYS cc_start: 0.6626 (pttt) cc_final: 0.6144 (tppt) REVERT: D 171 ILE cc_start: 0.8536 (tp) cc_final: 0.8260 (tt) REVERT: D 203 ILE cc_start: 0.6787 (mm) cc_final: 0.6009 (mm) REVERT: D 208 PHE cc_start: 0.7479 (p90) cc_final: 0.7075 (p90) REVERT: D 357 ARG cc_start: 0.6982 (mtp85) cc_final: 0.6725 (mtp85) REVERT: D 415 THR cc_start: 0.8509 (t) cc_final: 0.8168 (t) REVERT: D 417 ASN cc_start: 0.8193 (m-40) cc_final: 0.7786 (m110) REVERT: D 460 LYS cc_start: 0.5285 (ptpp) cc_final: 0.4165 (tppt) REVERT: E 119 GLU cc_start: 0.5910 (tt0) cc_final: 0.5229 (tm-30) REVERT: E 184 ARG cc_start: 0.6973 (mpt180) cc_final: 0.4995 (ttp80) REVERT: E 204 ARG cc_start: 0.6268 (mtt90) cc_final: 0.5979 (mmt90) REVERT: E 205 ARG cc_start: 0.6964 (mmt-90) cc_final: 0.6704 (mtp85) REVERT: E 228 ARG cc_start: 0.6617 (mmm-85) cc_final: 0.5565 (mmm160) REVERT: F 70 PRO cc_start: 0.5273 (Cg_exo) cc_final: 0.4922 (Cg_endo) REVERT: F 95 MET cc_start: 0.4754 (pmm) cc_final: 0.4464 (mpp) REVERT: F 118 ILE cc_start: 0.6373 (mm) cc_final: 0.6161 (mt) REVERT: F 143 LEU cc_start: 0.5668 (mt) cc_final: 0.5192 (tt) REVERT: G 68 PHE cc_start: 0.4136 (t80) cc_final: 0.3303 (t80) REVERT: G 117 THR cc_start: 0.7797 (p) cc_final: 0.7409 (t) REVERT: G 124 ILE cc_start: 0.7616 (tp) cc_final: 0.7346 (tp) REVERT: G 185 ASN cc_start: 0.7147 (t0) cc_final: 0.6811 (p0) REVERT: G 192 GLN cc_start: 0.5734 (mp10) cc_final: 0.4963 (mp10) REVERT: G 210 TRP cc_start: 0.6296 (t-100) cc_final: 0.6077 (t-100) REVERT: H 157 ASP cc_start: 0.7717 (m-30) cc_final: 0.7413 (m-30) REVERT: H 252 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6996 (mm-30) REVERT: H 259 MET cc_start: 0.7786 (mmt) cc_final: 0.7369 (mmt) REVERT: H 363 GLN cc_start: 0.8288 (tp40) cc_final: 0.7895 (tp-100) REVERT: H 364 ASP cc_start: 0.7474 (t0) cc_final: 0.7052 (m-30) REVERT: I 32 ASP cc_start: 0.7633 (m-30) cc_final: 0.7413 (m-30) REVERT: I 49 GLU cc_start: 0.6840 (tt0) cc_final: 0.6596 (mm-30) REVERT: I 78 LYS cc_start: 0.6892 (pttp) cc_final: 0.6016 (mttm) REVERT: I 94 TYR cc_start: 0.7876 (m-80) cc_final: 0.7425 (m-80) REVERT: I 155 GLU cc_start: 0.7542 (tt0) cc_final: 0.7114 (tt0) REVERT: I 195 ASP cc_start: 0.7598 (m-30) cc_final: 0.7365 (m-30) REVERT: I 202 ASN cc_start: 0.7322 (p0) cc_final: 0.6930 (p0) REVERT: I 266 PHE cc_start: 0.8203 (p90) cc_final: 0.7969 (p90) REVERT: I 315 LEU cc_start: 0.8005 (tt) cc_final: 0.7655 (tt) REVERT: I 336 LYS cc_start: 0.4714 (pttt) cc_final: 0.3863 (ptpp) REVERT: I 368 MET cc_start: 0.8330 (ttp) cc_final: 0.8059 (ttp) REVERT: I 412 PRO cc_start: 0.8012 (Cg_exo) cc_final: 0.7730 (Cg_endo) REVERT: J 22 TYR cc_start: 0.6423 (t80) cc_final: 0.5723 (t80) REVERT: J 29 LYS cc_start: 0.6178 (mttt) cc_final: 0.5796 (ttpt) REVERT: J 94 TYR cc_start: 0.6833 (m-80) cc_final: 0.6565 (m-80) REVERT: J 229 THR cc_start: 0.8126 (t) cc_final: 0.7767 (m) REVERT: K 328 VAL cc_start: 0.7767 (t) cc_final: 0.6946 (p) REVERT: O 426 MET cc_start: -0.1361 (ttt) cc_final: -0.1670 (ptt) outliers start: 6 outliers final: 0 residues processed: 789 average time/residue: 0.2302 time to fit residues: 293.8571 Evaluate side-chains 547 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 387 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 386 optimal weight: 0.0070 chunk 100 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 303 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 overall best weight: 3.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS A 426 GLN B 112 ASN B 264 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS C 181 ASN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 GLN E 66 GLN E 130 ASN G 233 ASN H 146 GLN H 153 GLN ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 398 GLN J 146 GLN K 209 GLN ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.152294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117562 restraints weight = 61535.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117384 restraints weight = 57213.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118259 restraints weight = 37896.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117795 restraints weight = 27317.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117972 restraints weight = 28647.575| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 35604 Z= 0.197 Angle : 0.695 14.903 48228 Z= 0.358 Chirality : 0.047 0.234 5233 Planarity : 0.006 0.083 6307 Dihedral : 5.524 32.891 4819 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.20 % Favored : 92.76 % Rotamer: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.12), residues: 4350 helix: 0.12 (0.12), residues: 1742 sheet: -1.64 (0.18), residues: 654 loop : -2.24 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 240 TYR 0.039 0.002 TYR H 77 PHE 0.033 0.002 PHE O 332 TRP 0.044 0.002 TRP K 365 HIS 0.012 0.002 HIS J 291 Details of bonding type rmsd covalent geometry : bond 0.00456 (35601) covalent geometry : angle 0.69517 (48224) SS BOND : bond 0.00527 ( 2) SS BOND : angle 1.75813 ( 4) hydrogen bonds : bond 0.04277 ( 1457) hydrogen bonds : angle 5.11736 ( 4152) Misc. bond : bond 0.00443 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 725 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7439 (p0) cc_final: 0.6997 (t70) REVERT: A 172 LYS cc_start: 0.6670 (tptm) cc_final: 0.5124 (ptpt) REVERT: A 184 ARG cc_start: 0.7083 (mmp-170) cc_final: 0.6765 (mmp-170) REVERT: A 279 LYS cc_start: 0.7778 (tptp) cc_final: 0.6767 (mmtt) REVERT: A 301 GLN cc_start: 0.8066 (tp40) cc_final: 0.7728 (tp40) REVERT: A 447 LYS cc_start: 0.6949 (ttpp) cc_final: 0.6417 (ttmm) REVERT: B 103 ASP cc_start: 0.7735 (m-30) cc_final: 0.7346 (m-30) REVERT: B 122 PHE cc_start: 0.8541 (m-80) cc_final: 0.8181 (m-80) REVERT: B 162 TYR cc_start: 0.8506 (m-80) cc_final: 0.7961 (m-80) REVERT: B 224 LYS cc_start: 0.7775 (tttt) cc_final: 0.7335 (mmtm) REVERT: B 261 ILE cc_start: 0.9076 (pt) cc_final: 0.8852 (tt) REVERT: B 302 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.7180 (tpp80) REVERT: B 336 LYS cc_start: 0.6454 (pttt) cc_final: 0.5366 (ttpt) REVERT: B 385 PRO cc_start: 0.8993 (Cg_endo) cc_final: 0.8725 (Cg_exo) REVERT: C 120 ASN cc_start: 0.8076 (p0) cc_final: 0.7846 (p0) REVERT: C 128 ARG cc_start: 0.6810 (tpp80) cc_final: 0.6520 (ttt-90) REVERT: C 336 LYS cc_start: 0.7470 (mtmt) cc_final: 0.6925 (mtmm) REVERT: D 125 LYS cc_start: 0.6627 (pttt) cc_final: 0.6140 (tppt) REVERT: D 171 ILE cc_start: 0.8619 (tp) cc_final: 0.8287 (tt) REVERT: D 206 GLN cc_start: 0.7628 (mp10) cc_final: 0.7314 (mp10) REVERT: D 336 LYS cc_start: 0.5542 (tttt) cc_final: 0.5173 (ttpt) REVERT: D 415 THR cc_start: 0.8586 (t) cc_final: 0.8279 (t) REVERT: D 417 ASN cc_start: 0.8093 (m-40) cc_final: 0.7872 (m110) REVERT: E 95 MET cc_start: 0.7478 (mmp) cc_final: 0.7166 (mmt) REVERT: E 113 PHE cc_start: 0.5696 (m-80) cc_final: 0.5344 (m-80) REVERT: E 120 GLU cc_start: 0.5832 (mt-10) cc_final: 0.5602 (mm-30) REVERT: E 184 ARG cc_start: 0.6912 (mpt180) cc_final: 0.4917 (ttp80) REVERT: E 189 LYS cc_start: 0.3716 (mttt) cc_final: 0.3231 (mmtt) REVERT: E 205 ARG cc_start: 0.6903 (mmt-90) cc_final: 0.6642 (mtp85) REVERT: E 228 ARG cc_start: 0.6743 (mmm-85) cc_final: 0.5499 (mmm160) REVERT: F 95 MET cc_start: 0.4833 (pmm) cc_final: 0.4563 (mpp) REVERT: F 118 ILE cc_start: 0.6435 (mm) cc_final: 0.6161 (tt) REVERT: G 127 ILE cc_start: 0.8726 (tp) cc_final: 0.8469 (tt) REVERT: H 252 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6910 (mm-30) REVERT: I 78 LYS cc_start: 0.7062 (pttp) cc_final: 0.6138 (mttt) REVERT: I 155 GLU cc_start: 0.7453 (tt0) cc_final: 0.7125 (tt0) REVERT: I 336 LYS cc_start: 0.4672 (pttt) cc_final: 0.3692 (ptpp) REVERT: I 363 GLN cc_start: 0.9133 (tp40) cc_final: 0.8562 (tp40) REVERT: I 380 HIS cc_start: 0.5960 (p-80) cc_final: 0.5517 (p90) REVERT: I 412 PRO cc_start: 0.7973 (Cg_exo) cc_final: 0.7629 (Cg_endo) REVERT: J 29 LYS cc_start: 0.6388 (mttt) cc_final: 0.6079 (ttpt) REVERT: J 48 ASP cc_start: 0.7193 (m-30) cc_final: 0.6940 (m-30) REVERT: J 95 PHE cc_start: 0.6784 (m-80) cc_final: 0.6285 (m-10) REVERT: J 187 TYR cc_start: 0.7872 (t80) cc_final: 0.7590 (t80) REVERT: J 229 THR cc_start: 0.8308 (t) cc_final: 0.7996 (m) REVERT: J 299 ASP cc_start: 0.7796 (p0) cc_final: 0.7384 (p0) REVERT: J 435 TYR cc_start: 0.1417 (t80) cc_final: 0.0803 (t80) REVERT: K 77 TYR cc_start: 0.6486 (m-10) cc_final: 0.6180 (m-10) REVERT: K 302 ARG cc_start: 0.6796 (ptm160) cc_final: 0.5961 (mtt90) REVERT: K 336 LYS cc_start: 0.5695 (pttt) cc_final: 0.4865 (ptpt) outliers start: 4 outliers final: 1 residues processed: 728 average time/residue: 0.2338 time to fit residues: 273.6833 Evaluate side-chains 509 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 508 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 296 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 424 optimal weight: 30.0000 chunk 288 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 414 optimal weight: 0.7980 chunk 380 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN G 173 GLN H 153 GLN ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 380 HIS ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 ASN J 206 GLN ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN K 150 HIS ** K 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 380 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.151661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115288 restraints weight = 61013.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113700 restraints weight = 47547.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113726 restraints weight = 41269.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114086 restraints weight = 38195.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114259 restraints weight = 32616.538| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35604 Z= 0.183 Angle : 0.670 13.731 48228 Z= 0.344 Chirality : 0.046 0.267 5233 Planarity : 0.006 0.062 6307 Dihedral : 5.389 30.099 4819 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.01 % Favored : 92.94 % Rotamer: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.12), residues: 4350 helix: 0.39 (0.12), residues: 1737 sheet: -1.44 (0.18), residues: 650 loop : -2.18 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 387 TYR 0.022 0.002 TYR H 22 PHE 0.044 0.002 PHE O 332 TRP 0.038 0.002 TRP K 365 HIS 0.007 0.001 HIS E 147 Details of bonding type rmsd covalent geometry : bond 0.00425 (35601) covalent geometry : angle 0.66945 (48224) SS BOND : bond 0.00814 ( 2) SS BOND : angle 1.86560 ( 4) hydrogen bonds : bond 0.03998 ( 1457) hydrogen bonds : angle 4.96868 ( 4152) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 691 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7683 (p0) cc_final: 0.7220 (t70) REVERT: A 125 LYS cc_start: 0.6518 (tttt) cc_final: 0.6085 (ptpt) REVERT: A 184 ARG cc_start: 0.6920 (mmp-170) cc_final: 0.6629 (mmp-170) REVERT: A 224 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7721 (mttp) REVERT: A 279 LYS cc_start: 0.7953 (tptp) cc_final: 0.6891 (mmtt) REVERT: A 315 LEU cc_start: 0.8947 (tt) cc_final: 0.8729 (tt) REVERT: A 447 LYS cc_start: 0.6828 (ttpp) cc_final: 0.6571 (ttmm) REVERT: B 103 ASP cc_start: 0.7898 (m-30) cc_final: 0.7417 (m-30) REVERT: B 122 PHE cc_start: 0.8507 (m-80) cc_final: 0.8199 (m-80) REVERT: B 162 TYR cc_start: 0.8537 (m-80) cc_final: 0.7919 (m-80) REVERT: B 224 LYS cc_start: 0.7584 (tttt) cc_final: 0.7308 (mmtm) REVERT: B 302 ARG cc_start: 0.7544 (ttm-80) cc_final: 0.7184 (tpp80) REVERT: B 336 LYS cc_start: 0.6490 (pttt) cc_final: 0.5500 (ttpt) REVERT: B 354 ASP cc_start: 0.5436 (t70) cc_final: 0.4925 (t0) REVERT: B 385 PRO cc_start: 0.9016 (Cg_endo) cc_final: 0.8750 (Cg_exo) REVERT: C 48 ASP cc_start: 0.7628 (m-30) cc_final: 0.7124 (m-30) REVERT: C 120 ASN cc_start: 0.8125 (p0) cc_final: 0.7899 (p0) REVERT: C 128 ARG cc_start: 0.6877 (tpp80) cc_final: 0.6536 (ttt-90) REVERT: C 336 LYS cc_start: 0.7384 (mtmt) cc_final: 0.7010 (mtmm) REVERT: D 125 LYS cc_start: 0.6480 (pttt) cc_final: 0.6264 (mmtm) REVERT: D 206 GLN cc_start: 0.7939 (mp10) cc_final: 0.7433 (mp10) REVERT: D 415 THR cc_start: 0.8594 (t) cc_final: 0.8329 (t) REVERT: E 95 MET cc_start: 0.7442 (mmp) cc_final: 0.7205 (mmt) REVERT: E 113 PHE cc_start: 0.5781 (m-80) cc_final: 0.5519 (m-80) REVERT: E 120 GLU cc_start: 0.5829 (mt-10) cc_final: 0.5594 (mm-30) REVERT: E 184 ARG cc_start: 0.6700 (mpt180) cc_final: 0.4687 (ttp80) REVERT: E 189 LYS cc_start: 0.3654 (mttt) cc_final: 0.3009 (mmtt) REVERT: E 205 ARG cc_start: 0.7065 (mmt-90) cc_final: 0.6824 (mtp85) REVERT: E 228 ARG cc_start: 0.6751 (mmm-85) cc_final: 0.5375 (mmm160) REVERT: F 95 MET cc_start: 0.5106 (pmm) cc_final: 0.4903 (mpp) REVERT: F 118 ILE cc_start: 0.6541 (mm) cc_final: 0.6282 (mt) REVERT: F 143 LEU cc_start: 0.6077 (mt) cc_final: 0.5422 (tt) REVERT: G 99 PHE cc_start: 0.7208 (p90) cc_final: 0.6994 (p90) REVERT: G 210 TRP cc_start: 0.6859 (t-100) cc_final: 0.6189 (t-100) REVERT: H 252 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6844 (mt-10) REVERT: H 339 THR cc_start: 0.8217 (m) cc_final: 0.7834 (t) REVERT: I 78 LYS cc_start: 0.7205 (pttp) cc_final: 0.6073 (mttt) REVERT: I 124 PHE cc_start: 0.6866 (t80) cc_final: 0.6658 (t80) REVERT: I 135 ILE cc_start: 0.7986 (mp) cc_final: 0.7691 (mp) REVERT: I 155 GLU cc_start: 0.7538 (tt0) cc_final: 0.7251 (tt0) REVERT: I 336 LYS cc_start: 0.4463 (pttt) cc_final: 0.3461 (ptpp) REVERT: I 363 GLN cc_start: 0.9149 (tp40) cc_final: 0.8564 (tp40) REVERT: I 412 PRO cc_start: 0.7613 (Cg_exo) cc_final: 0.7253 (Cg_endo) REVERT: J 29 LYS cc_start: 0.6367 (mttt) cc_final: 0.6069 (ttpt) REVERT: J 95 PHE cc_start: 0.6871 (m-80) cc_final: 0.6246 (m-10) REVERT: J 187 TYR cc_start: 0.7912 (t80) cc_final: 0.7684 (t80) REVERT: J 229 THR cc_start: 0.8318 (t) cc_final: 0.8070 (m) REVERT: J 294 MET cc_start: 0.7455 (tpp) cc_final: 0.7249 (ttm) REVERT: J 299 ASP cc_start: 0.7933 (p0) cc_final: 0.7428 (p0) REVERT: J 342 PHE cc_start: 0.7435 (p90) cc_final: 0.7223 (p90) REVERT: K 117 ILE cc_start: 0.9247 (mm) cc_final: 0.9040 (mm) REVERT: K 302 ARG cc_start: 0.6910 (ptm160) cc_final: 0.6058 (mtt90) REVERT: K 336 LYS cc_start: 0.5924 (pttt) cc_final: 0.4996 (ptpt) REVERT: K 365 TRP cc_start: 0.6981 (m100) cc_final: 0.6655 (m100) REVERT: K 437 GLU cc_start: 0.3924 (mp0) cc_final: 0.3074 (mm-30) outliers start: 2 outliers final: 0 residues processed: 693 average time/residue: 0.2300 time to fit residues: 257.6734 Evaluate side-chains 513 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 35 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 277 optimal weight: 9.9990 chunk 342 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 403 optimal weight: 50.0000 chunk 339 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 343 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN E 233 ASN G 173 GLN H 181 ASN ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 GLN ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 GLN ** K 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115174 restraints weight = 61674.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113801 restraints weight = 61284.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115401 restraints weight = 44319.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115343 restraints weight = 32204.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115473 restraints weight = 31025.639| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35604 Z= 0.215 Angle : 0.709 14.818 48228 Z= 0.362 Chirality : 0.047 0.258 5233 Planarity : 0.006 0.069 6307 Dihedral : 5.483 27.507 4819 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.75 % Favored : 92.21 % Rotamer: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.12), residues: 4350 helix: 0.25 (0.12), residues: 1763 sheet: -1.28 (0.18), residues: 650 loop : -2.17 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 292 TYR 0.023 0.002 TYR H 236 PHE 0.043 0.002 PHE O 332 TRP 0.030 0.002 TRP K 365 HIS 0.007 0.001 HIS K 295 Details of bonding type rmsd covalent geometry : bond 0.00500 (35601) covalent geometry : angle 0.70877 (48224) SS BOND : bond 0.00288 ( 2) SS BOND : angle 2.49604 ( 4) hydrogen bonds : bond 0.04264 ( 1457) hydrogen bonds : angle 5.02572 ( 4152) Misc. bond : bond 0.00188 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 657 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7576 (p0) cc_final: 0.7217 (t70) REVERT: A 184 ARG cc_start: 0.6882 (mmp-170) cc_final: 0.6635 (mmp-170) REVERT: A 224 LYS cc_start: 0.8158 (ttmm) cc_final: 0.7770 (mttp) REVERT: A 279 LYS cc_start: 0.8050 (tptp) cc_final: 0.6838 (mmtt) REVERT: A 315 LEU cc_start: 0.8985 (tt) cc_final: 0.8785 (tt) REVERT: B 103 ASP cc_start: 0.7871 (m-30) cc_final: 0.7462 (m-30) REVERT: B 122 PHE cc_start: 0.8459 (m-80) cc_final: 0.8191 (m-80) REVERT: B 224 LYS cc_start: 0.7666 (tttt) cc_final: 0.7386 (mmtm) REVERT: B 302 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.7106 (tpp80) REVERT: B 336 LYS cc_start: 0.6441 (pttt) cc_final: 0.5519 (ttpt) REVERT: B 354 ASP cc_start: 0.5555 (t70) cc_final: 0.5000 (t0) REVERT: B 385 PRO cc_start: 0.9006 (Cg_endo) cc_final: 0.8686 (Cg_exo) REVERT: C 48 ASP cc_start: 0.7462 (m-30) cc_final: 0.6935 (m-30) REVERT: C 128 ARG cc_start: 0.6901 (tpp80) cc_final: 0.6388 (ttt-90) REVERT: C 155 GLU cc_start: 0.8108 (pp20) cc_final: 0.7825 (pp20) REVERT: C 336 LYS cc_start: 0.7439 (mtmt) cc_final: 0.7121 (mtmm) REVERT: D 206 GLN cc_start: 0.8164 (mp10) cc_final: 0.7577 (mp10) REVERT: D 300 ARG cc_start: 0.6436 (tpt90) cc_final: 0.6077 (tpt170) REVERT: D 415 THR cc_start: 0.8668 (t) cc_final: 0.8358 (t) REVERT: E 113 PHE cc_start: 0.5624 (m-80) cc_final: 0.5417 (m-80) REVERT: E 179 THR cc_start: 0.8253 (p) cc_final: 0.7923 (t) REVERT: E 184 ARG cc_start: 0.6870 (mpt180) cc_final: 0.4788 (ttp80) REVERT: E 205 ARG cc_start: 0.6861 (mmt-90) cc_final: 0.6508 (mtp85) REVERT: E 228 ARG cc_start: 0.6745 (mmm-85) cc_final: 0.5399 (mmm-85) REVERT: F 95 MET cc_start: 0.4923 (pmm) cc_final: 0.4682 (mpp) REVERT: F 118 ILE cc_start: 0.6517 (mm) cc_final: 0.6241 (tt) REVERT: F 143 LEU cc_start: 0.5925 (mt) cc_final: 0.5223 (tt) REVERT: F 186 ILE cc_start: 0.5523 (tt) cc_final: 0.5155 (tp) REVERT: G 99 PHE cc_start: 0.7213 (p90) cc_final: 0.6926 (p90) REVERT: G 210 TRP cc_start: 0.6836 (t-100) cc_final: 0.6368 (t-100) REVERT: H 252 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6765 (mt-10) REVERT: H 256 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7532 (tm-30) REVERT: I 78 LYS cc_start: 0.7326 (pttp) cc_final: 0.6207 (mttm) REVERT: I 155 GLU cc_start: 0.7522 (tt0) cc_final: 0.7291 (tt0) REVERT: I 336 LYS cc_start: 0.4588 (pttt) cc_final: 0.3531 (ptpp) REVERT: I 363 GLN cc_start: 0.9088 (tp40) cc_final: 0.8509 (tp40) REVERT: I 412 PRO cc_start: 0.7766 (Cg_exo) cc_final: 0.7411 (Cg_endo) REVERT: J 29 LYS cc_start: 0.6500 (mttt) cc_final: 0.5995 (ttpt) REVERT: J 90 GLU cc_start: 0.6309 (tm-30) cc_final: 0.5795 (tm-30) REVERT: J 95 PHE cc_start: 0.6748 (m-80) cc_final: 0.6170 (m-10) REVERT: J 187 TYR cc_start: 0.7922 (t80) cc_final: 0.7712 (t80) REVERT: J 229 THR cc_start: 0.8365 (t) cc_final: 0.8114 (m) REVERT: J 294 MET cc_start: 0.7519 (tpp) cc_final: 0.7291 (ttm) REVERT: J 299 ASP cc_start: 0.8010 (p0) cc_final: 0.7467 (p0) REVERT: K 186 VAL cc_start: 0.8177 (t) cc_final: 0.7881 (p) REVERT: K 288 LEU cc_start: 0.9321 (tp) cc_final: 0.8954 (tt) REVERT: K 365 TRP cc_start: 0.7519 (m100) cc_final: 0.7302 (m100) REVERT: K 437 GLU cc_start: 0.3835 (mp0) cc_final: 0.2941 (mm-30) REVERT: M 409 LEU cc_start: 0.2990 (mt) cc_final: 0.2094 (tt) outliers start: 1 outliers final: 0 residues processed: 658 average time/residue: 0.2308 time to fit residues: 245.0932 Evaluate side-chains 500 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 345 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 178 optimal weight: 20.0000 chunk 330 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 258 ASN G 173 GLN ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN K 209 GLN ** K 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 HIS ** K 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 390 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112079 restraints weight = 61890.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110074 restraints weight = 43253.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110506 restraints weight = 33681.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110718 restraints weight = 32445.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111014 restraints weight = 28571.010| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 35604 Z= 0.262 Angle : 0.759 14.300 48228 Z= 0.390 Chirality : 0.049 0.242 5233 Planarity : 0.007 0.089 6307 Dihedral : 5.744 30.639 4819 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.32 % Favored : 91.63 % Rotamer: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.12), residues: 4350 helix: 0.03 (0.12), residues: 1758 sheet: -1.10 (0.19), residues: 632 loop : -2.20 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 316 TYR 0.023 0.002 TYR A 22 PHE 0.039 0.003 PHE O 332 TRP 0.018 0.002 TRP I 408 HIS 0.011 0.002 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00612 (35601) covalent geometry : angle 0.75849 (48224) SS BOND : bond 0.00742 ( 2) SS BOND : angle 2.47714 ( 4) hydrogen bonds : bond 0.04582 ( 1457) hydrogen bonds : angle 5.19407 ( 4152) Misc. bond : bond 0.00469 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 643 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7531 (p0) cc_final: 0.7254 (t70) REVERT: A 125 LYS cc_start: 0.6612 (tttt) cc_final: 0.6010 (ptpt) REVERT: A 184 ARG cc_start: 0.6898 (mmp-170) cc_final: 0.6627 (mmp-170) REVERT: A 224 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7832 (mttp) REVERT: A 279 LYS cc_start: 0.8311 (tptp) cc_final: 0.6910 (mttt) REVERT: A 315 LEU cc_start: 0.8995 (tt) cc_final: 0.8793 (tt) REVERT: B 103 ASP cc_start: 0.7930 (m-30) cc_final: 0.7561 (m-30) REVERT: B 107 GLU cc_start: 0.7615 (pm20) cc_final: 0.7151 (pt0) REVERT: B 224 LYS cc_start: 0.7576 (tttt) cc_final: 0.7288 (mmtm) REVERT: B 302 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7215 (tpp80) REVERT: B 336 LYS cc_start: 0.6530 (pttt) cc_final: 0.5617 (ttpt) REVERT: B 385 PRO cc_start: 0.8940 (Cg_endo) cc_final: 0.8636 (Cg_exo) REVERT: C 48 ASP cc_start: 0.7668 (m-30) cc_final: 0.7207 (m-30) REVERT: C 128 ARG cc_start: 0.6983 (tpp80) cc_final: 0.6464 (ttt-90) REVERT: C 155 GLU cc_start: 0.8131 (pp20) cc_final: 0.7800 (pp20) REVERT: D 300 ARG cc_start: 0.6485 (tpt90) cc_final: 0.6137 (tpt170) REVERT: D 393 ASP cc_start: 0.7223 (m-30) cc_final: 0.6921 (m-30) REVERT: E 179 THR cc_start: 0.8264 (p) cc_final: 0.7909 (t) REVERT: E 205 ARG cc_start: 0.7004 (mmt-90) cc_final: 0.6615 (mtp85) REVERT: E 228 ARG cc_start: 0.6792 (mmm-85) cc_final: 0.5330 (mmm-85) REVERT: F 70 PRO cc_start: 0.5261 (Cg_exo) cc_final: 0.5010 (Cg_endo) REVERT: F 94 ARG cc_start: 0.6007 (mtt90) cc_final: 0.5801 (mtm-85) REVERT: F 118 ILE cc_start: 0.6645 (mm) cc_final: 0.6411 (mt) REVERT: F 143 LEU cc_start: 0.5953 (mt) cc_final: 0.5334 (tt) REVERT: G 99 PHE cc_start: 0.7326 (p90) cc_final: 0.7052 (p90) REVERT: G 204 ARG cc_start: 0.7422 (mmt180) cc_final: 0.6870 (mmt180) REVERT: G 210 TRP cc_start: 0.6639 (t-100) cc_final: 0.6176 (t-100) REVERT: G 232 GLU cc_start: 0.7003 (pt0) cc_final: 0.6682 (tp30) REVERT: H 128 ARG cc_start: 0.7216 (ttt180) cc_final: 0.6608 (tpt170) REVERT: H 133 GLU cc_start: 0.7164 (mp0) cc_final: 0.6807 (mp0) REVERT: H 252 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6709 (mt-10) REVERT: H 256 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7545 (tm-30) REVERT: H 384 MET cc_start: 0.7518 (ttm) cc_final: 0.7282 (ttt) REVERT: I 78 LYS cc_start: 0.7408 (pttp) cc_final: 0.6099 (mttm) REVERT: J 29 LYS cc_start: 0.6591 (mttt) cc_final: 0.5997 (ttpt) REVERT: J 49 GLU cc_start: 0.5539 (tp30) cc_final: 0.4203 (mm-30) REVERT: J 90 GLU cc_start: 0.6684 (tm-30) cc_final: 0.6321 (tm-30) REVERT: J 91 GLU cc_start: 0.6960 (pm20) cc_final: 0.6473 (pm20) REVERT: J 95 PHE cc_start: 0.6994 (m-80) cc_final: 0.6197 (m-10) REVERT: J 229 THR cc_start: 0.8465 (t) cc_final: 0.8221 (m) REVERT: J 236 TYR cc_start: 0.8164 (m-80) cc_final: 0.7958 (m-80) REVERT: J 290 ILE cc_start: 0.9280 (mm) cc_final: 0.9066 (mm) REVERT: J 299 ASP cc_start: 0.8133 (p0) cc_final: 0.7571 (p0) REVERT: K 259 MET cc_start: 0.8581 (mmm) cc_final: 0.8297 (mtt) REVERT: K 344 ASP cc_start: 0.7692 (t70) cc_final: 0.6815 (t70) REVERT: N 324 MET cc_start: 0.2528 (mmm) cc_final: 0.2250 (mmm) outliers start: 2 outliers final: 0 residues processed: 645 average time/residue: 0.1996 time to fit residues: 207.4816 Evaluate side-chains 506 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 279 optimal weight: 0.9990 chunk 280 optimal weight: 5.9990 chunk 333 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 319 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 328 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 322 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 ASN ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN K 209 GLN ** K 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 380 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.152330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116020 restraints weight = 61125.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114080 restraints weight = 40182.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114920 restraints weight = 34468.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115620 restraints weight = 31732.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115860 restraints weight = 26763.214| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35604 Z= 0.139 Angle : 0.644 12.998 48228 Z= 0.328 Chirality : 0.045 0.273 5233 Planarity : 0.006 0.079 6307 Dihedral : 5.311 29.828 4819 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.11 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.12), residues: 4350 helix: 0.41 (0.12), residues: 1766 sheet: -0.84 (0.19), residues: 632 loop : -2.08 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 292 TYR 0.026 0.002 TYR A 22 PHE 0.051 0.002 PHE O 332 TRP 0.038 0.001 TRP K 365 HIS 0.011 0.001 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00323 (35601) covalent geometry : angle 0.64330 (48224) SS BOND : bond 0.00578 ( 2) SS BOND : angle 2.12496 ( 4) hydrogen bonds : bond 0.03684 ( 1457) hydrogen bonds : angle 4.89340 ( 4152) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7345 (p0) cc_final: 0.7131 (t70) REVERT: A 42 GLN cc_start: 0.7290 (mm-40) cc_final: 0.7044 (tp40) REVERT: A 125 LYS cc_start: 0.6638 (tttt) cc_final: 0.6143 (ptpt) REVERT: A 184 ARG cc_start: 0.6864 (mmp-170) cc_final: 0.6530 (mmp-170) REVERT: A 224 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7756 (mttm) REVERT: A 279 LYS cc_start: 0.8136 (tptp) cc_final: 0.6805 (mttt) REVERT: A 315 LEU cc_start: 0.8940 (tt) cc_final: 0.8716 (tt) REVERT: B 103 ASP cc_start: 0.7842 (m-30) cc_final: 0.7473 (m-30) REVERT: B 224 LYS cc_start: 0.7494 (tttt) cc_final: 0.7205 (mmtm) REVERT: B 302 ARG cc_start: 0.7693 (ttm-80) cc_final: 0.7182 (tpp80) REVERT: B 336 LYS cc_start: 0.6542 (pttt) cc_final: 0.5565 (ttpt) REVERT: B 354 ASP cc_start: 0.5685 (t70) cc_final: 0.5075 (t0) REVERT: B 385 PRO cc_start: 0.8903 (Cg_endo) cc_final: 0.8583 (Cg_exo) REVERT: C 48 ASP cc_start: 0.7702 (m-30) cc_final: 0.7142 (m-30) REVERT: C 120 ASN cc_start: 0.8296 (p0) cc_final: 0.8076 (p0) REVERT: C 128 ARG cc_start: 0.6925 (tpp80) cc_final: 0.6527 (ttt-90) REVERT: D 203 ILE cc_start: 0.6452 (mm) cc_final: 0.6043 (tt) REVERT: D 204 ASN cc_start: 0.7854 (p0) cc_final: 0.7633 (p0) REVERT: D 206 GLN cc_start: 0.7880 (mp-120) cc_final: 0.7073 (mp10) REVERT: D 393 ASP cc_start: 0.7209 (m-30) cc_final: 0.6825 (m-30) REVERT: D 415 THR cc_start: 0.8545 (t) cc_final: 0.8233 (t) REVERT: E 120 GLU cc_start: 0.6023 (mt-10) cc_final: 0.5641 (mm-30) REVERT: E 129 GLN cc_start: 0.7195 (mt0) cc_final: 0.6904 (mp10) REVERT: E 179 THR cc_start: 0.8202 (p) cc_final: 0.7845 (t) REVERT: E 202 PRO cc_start: 0.6070 (Cg_endo) cc_final: 0.5804 (Cg_exo) REVERT: E 205 ARG cc_start: 0.6974 (mmt-90) cc_final: 0.6578 (mtp85) REVERT: E 228 ARG cc_start: 0.6787 (mmm-85) cc_final: 0.5326 (mmm-85) REVERT: F 70 PRO cc_start: 0.5060 (Cg_exo) cc_final: 0.4762 (Cg_endo) REVERT: F 118 ILE cc_start: 0.6620 (mm) cc_final: 0.6338 (mt) REVERT: F 143 LEU cc_start: 0.5959 (mt) cc_final: 0.5380 (tt) REVERT: G 99 PHE cc_start: 0.7113 (p90) cc_final: 0.6857 (p90) REVERT: G 204 ARG cc_start: 0.7325 (mmt180) cc_final: 0.6811 (mmt180) REVERT: G 210 TRP cc_start: 0.6572 (t-100) cc_final: 0.6129 (t-100) REVERT: H 95 PHE cc_start: 0.6122 (m-80) cc_final: 0.5846 (m-80) REVERT: H 128 ARG cc_start: 0.7103 (ttt180) cc_final: 0.6606 (tpt170) REVERT: H 133 GLU cc_start: 0.7192 (mp0) cc_final: 0.6878 (mp0) REVERT: H 252 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6753 (mt-10) REVERT: I 78 LYS cc_start: 0.7371 (pttp) cc_final: 0.6105 (mttm) REVERT: I 85 GLU cc_start: 0.7799 (pm20) cc_final: 0.7456 (pm20) REVERT: I 208 PHE cc_start: 0.7070 (m-10) cc_final: 0.6504 (m-10) REVERT: J 29 LYS cc_start: 0.6480 (mttt) cc_final: 0.6105 (tttt) REVERT: J 49 GLU cc_start: 0.5594 (tp30) cc_final: 0.4247 (mm-30) REVERT: J 90 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6279 (tm-30) REVERT: J 95 PHE cc_start: 0.6923 (m-80) cc_final: 0.6205 (m-10) REVERT: J 104 LEU cc_start: 0.7518 (mp) cc_final: 0.7041 (tp) REVERT: J 172 LYS cc_start: 0.6072 (mtmm) cc_final: 0.5634 (tptp) REVERT: J 229 THR cc_start: 0.8417 (t) cc_final: 0.8217 (m) REVERT: J 299 ASP cc_start: 0.8052 (p0) cc_final: 0.7516 (p0) REVERT: J 300 ARG cc_start: 0.7653 (tpt90) cc_final: 0.7390 (tpt90) REVERT: K 171 ILE cc_start: 0.8231 (mp) cc_final: 0.8017 (mp) REVERT: K 186 VAL cc_start: 0.8088 (t) cc_final: 0.7846 (p) REVERT: K 259 MET cc_start: 0.8552 (mmm) cc_final: 0.8260 (mtt) REVERT: K 344 ASP cc_start: 0.7323 (t70) cc_final: 0.6909 (t70) REVERT: K 437 GLU cc_start: 0.3640 (mp0) cc_final: 0.3074 (mm-30) REVERT: N 324 MET cc_start: 0.2568 (mmm) cc_final: 0.2115 (mmp) REVERT: O 324 MET cc_start: 0.0262 (tpp) cc_final: -0.1312 (mtm) outliers start: 0 outliers final: 0 residues processed: 695 average time/residue: 0.2242 time to fit residues: 253.1974 Evaluate side-chains 528 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 270 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 394 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 354 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 380 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS B 112 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 209 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 HIS E 258 ASN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.149696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113408 restraints weight = 61235.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111147 restraints weight = 43209.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112444 restraints weight = 35598.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112631 restraints weight = 27910.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112808 restraints weight = 26456.801| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35604 Z= 0.219 Angle : 0.725 14.353 48228 Z= 0.371 Chirality : 0.048 0.293 5233 Planarity : 0.006 0.084 6307 Dihedral : 5.579 29.264 4819 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.79 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.12), residues: 4350 helix: 0.28 (0.12), residues: 1757 sheet: -0.84 (0.19), residues: 634 loop : -2.08 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 292 TYR 0.030 0.002 TYR J 236 PHE 0.048 0.002 PHE O 332 TRP 0.036 0.002 TRP L 350 HIS 0.010 0.002 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00513 (35601) covalent geometry : angle 0.72469 (48224) SS BOND : bond 0.00728 ( 2) SS BOND : angle 2.26496 ( 4) hydrogen bonds : bond 0.04285 ( 1457) hydrogen bonds : angle 5.04516 ( 4152) Misc. bond : bond 0.00087 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 621 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ARG cc_start: 0.6840 (mmp-170) cc_final: 0.6534 (mmp-170) REVERT: A 224 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7833 (mttp) REVERT: A 279 LYS cc_start: 0.8267 (tptp) cc_final: 0.6842 (mttt) REVERT: B 103 ASP cc_start: 0.7912 (m-30) cc_final: 0.7523 (m-30) REVERT: B 224 LYS cc_start: 0.7529 (tttt) cc_final: 0.7223 (mmtm) REVERT: B 302 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7280 (tpp80) REVERT: B 336 LYS cc_start: 0.6616 (pttt) cc_final: 0.5651 (ttpt) REVERT: B 440 ASP cc_start: 0.6600 (p0) cc_final: 0.6353 (m-30) REVERT: C 48 ASP cc_start: 0.7731 (m-30) cc_final: 0.7196 (m-30) REVERT: C 128 ARG cc_start: 0.6913 (tpp80) cc_final: 0.6551 (ttt-90) REVERT: D 95 PHE cc_start: 0.7968 (m-80) cc_final: 0.7732 (m-80) REVERT: D 393 ASP cc_start: 0.7414 (m-30) cc_final: 0.7053 (m-30) REVERT: D 415 THR cc_start: 0.8609 (t) cc_final: 0.8322 (t) REVERT: E 91 LEU cc_start: 0.7715 (tp) cc_final: 0.7425 (tt) REVERT: E 99 PHE cc_start: 0.7607 (p90) cc_final: 0.7406 (p90) REVERT: E 120 GLU cc_start: 0.6128 (mt-10) cc_final: 0.5647 (mm-30) REVERT: E 179 THR cc_start: 0.8228 (p) cc_final: 0.7930 (t) REVERT: E 184 ARG cc_start: 0.6698 (mpt180) cc_final: 0.4662 (ttp80) REVERT: E 202 PRO cc_start: 0.6137 (Cg_endo) cc_final: 0.5837 (Cg_exo) REVERT: E 205 ARG cc_start: 0.7017 (mmt-90) cc_final: 0.6588 (mtp85) REVERT: E 208 VAL cc_start: 0.7539 (p) cc_final: 0.7279 (p) REVERT: E 228 ARG cc_start: 0.6712 (mmm-85) cc_final: 0.5299 (mmm-85) REVERT: F 70 PRO cc_start: 0.5154 (Cg_exo) cc_final: 0.4850 (Cg_endo) REVERT: F 143 LEU cc_start: 0.5866 (mt) cc_final: 0.5283 (tt) REVERT: G 99 PHE cc_start: 0.7293 (p90) cc_final: 0.6997 (p90) REVERT: G 204 ARG cc_start: 0.7355 (mmt180) cc_final: 0.6825 (mmt180) REVERT: G 210 TRP cc_start: 0.6529 (t-100) cc_final: 0.6120 (t-100) REVERT: H 95 PHE cc_start: 0.6254 (m-80) cc_final: 0.5975 (m-80) REVERT: H 133 GLU cc_start: 0.7262 (mp0) cc_final: 0.6907 (mp0) REVERT: H 252 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6728 (mt-10) REVERT: I 78 LYS cc_start: 0.7522 (pttp) cc_final: 0.6169 (mttm) REVERT: I 117 ILE cc_start: 0.9054 (tp) cc_final: 0.8789 (tt) REVERT: I 155 GLU cc_start: 0.7699 (tt0) cc_final: 0.7419 (tt0) REVERT: I 194 LEU cc_start: 0.6873 (mt) cc_final: 0.6646 (mt) REVERT: I 246 GLU cc_start: 0.8350 (pp20) cc_final: 0.7717 (pp20) REVERT: I 248 MET cc_start: 0.8748 (mmm) cc_final: 0.8445 (tpp) REVERT: I 363 GLN cc_start: 0.9187 (tp40) cc_final: 0.8574 (tp-100) REVERT: J 29 LYS cc_start: 0.6616 (mttt) cc_final: 0.6245 (tttt) REVERT: J 49 GLU cc_start: 0.5716 (tp30) cc_final: 0.4325 (mm-30) REVERT: J 90 GLU cc_start: 0.6737 (tm-30) cc_final: 0.6506 (tm-30) REVERT: J 91 GLU cc_start: 0.6984 (pm20) cc_final: 0.6543 (pm20) REVERT: J 95 PHE cc_start: 0.6960 (m-80) cc_final: 0.6186 (m-10) REVERT: J 172 LYS cc_start: 0.6125 (mtmm) cc_final: 0.5643 (tptp) REVERT: J 229 THR cc_start: 0.8498 (t) cc_final: 0.8266 (m) REVERT: J 299 ASP cc_start: 0.8112 (p0) cc_final: 0.7584 (p0) REVERT: J 300 ARG cc_start: 0.7742 (tpt90) cc_final: 0.7457 (tpt90) REVERT: J 354 ASP cc_start: 0.6830 (t70) cc_final: 0.6415 (m-30) REVERT: K 186 VAL cc_start: 0.8156 (t) cc_final: 0.7887 (p) REVERT: K 368 MET cc_start: 0.8080 (tpp) cc_final: 0.7858 (ttm) REVERT: N 324 MET cc_start: 0.2721 (mmm) cc_final: 0.2493 (mmm) REVERT: O 324 MET cc_start: 0.0246 (tpp) cc_final: -0.1285 (mtm) outliers start: 0 outliers final: 0 residues processed: 621 average time/residue: 0.1968 time to fit residues: 199.6608 Evaluate side-chains 485 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 172 optimal weight: 0.0570 chunk 159 optimal weight: 5.9990 chunk 330 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 365 optimal weight: 5.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 HIS E 258 ASN G 173 GLN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.151656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115525 restraints weight = 60775.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114124 restraints weight = 39798.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114698 restraints weight = 34299.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115152 restraints weight = 29683.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115372 restraints weight = 26375.083| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35604 Z= 0.148 Angle : 0.657 13.255 48228 Z= 0.336 Chirality : 0.046 0.288 5233 Planarity : 0.006 0.082 6307 Dihedral : 5.326 30.056 4819 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.67 % Favored : 93.31 % Rotamer: Outliers : 0.03 % Allowed : 0.69 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.12), residues: 4350 helix: 0.47 (0.12), residues: 1772 sheet: -0.78 (0.19), residues: 634 loop : -2.04 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.043 0.002 TYR I 22 PHE 0.044 0.002 PHE O 332 TRP 0.027 0.001 TRP K 365 HIS 0.021 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00346 (35601) covalent geometry : angle 0.65630 (48224) SS BOND : bond 0.00564 ( 2) SS BOND : angle 1.99554 ( 4) hydrogen bonds : bond 0.03703 ( 1457) hydrogen bonds : angle 4.87325 ( 4152) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 621 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ARG cc_start: 0.6797 (mmp-170) cc_final: 0.6472 (mmp-170) REVERT: A 224 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7774 (mttp) REVERT: A 279 LYS cc_start: 0.8133 (tptp) cc_final: 0.6860 (mmtt) REVERT: A 315 LEU cc_start: 0.8833 (tt) cc_final: 0.8506 (tt) REVERT: B 103 ASP cc_start: 0.7884 (m-30) cc_final: 0.7489 (m-30) REVERT: B 224 LYS cc_start: 0.7476 (tttt) cc_final: 0.7185 (mmtm) REVERT: B 302 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7256 (tpp80) REVERT: B 336 LYS cc_start: 0.6606 (pttt) cc_final: 0.5630 (ttpt) REVERT: B 354 ASP cc_start: 0.5712 (t70) cc_final: 0.5120 (t0) REVERT: B 385 PRO cc_start: 0.8886 (Cg_endo) cc_final: 0.8544 (Cg_exo) REVERT: B 440 ASP cc_start: 0.6556 (p0) cc_final: 0.6323 (m-30) REVERT: C 48 ASP cc_start: 0.7669 (m-30) cc_final: 0.7127 (m-30) REVERT: C 128 ARG cc_start: 0.6894 (tpp80) cc_final: 0.6674 (ttt-90) REVERT: D 95 PHE cc_start: 0.7922 (m-80) cc_final: 0.7632 (m-80) REVERT: D 203 ILE cc_start: 0.6437 (mm) cc_final: 0.6179 (tp) REVERT: D 393 ASP cc_start: 0.7325 (m-30) cc_final: 0.6932 (m-30) REVERT: D 415 THR cc_start: 0.8526 (t) cc_final: 0.8238 (t) REVERT: D 435 TYR cc_start: 0.6129 (t80) cc_final: 0.5848 (t80) REVERT: E 91 LEU cc_start: 0.7585 (tp) cc_final: 0.7304 (tt) REVERT: E 99 PHE cc_start: 0.7618 (p90) cc_final: 0.7388 (p90) REVERT: E 120 GLU cc_start: 0.6151 (mt-10) cc_final: 0.5719 (mm-30) REVERT: E 179 THR cc_start: 0.8198 (p) cc_final: 0.7894 (t) REVERT: E 184 ARG cc_start: 0.6648 (mpt180) cc_final: 0.4651 (ttp80) REVERT: E 202 PRO cc_start: 0.6030 (Cg_endo) cc_final: 0.5741 (Cg_exo) REVERT: E 205 ARG cc_start: 0.7044 (mmt-90) cc_final: 0.6597 (mtp85) REVERT: E 208 VAL cc_start: 0.7579 (p) cc_final: 0.7312 (p) REVERT: E 228 ARG cc_start: 0.6733 (mmm-85) cc_final: 0.5344 (mmm-85) REVERT: F 70 PRO cc_start: 0.5182 (Cg_exo) cc_final: 0.4874 (Cg_endo) REVERT: F 95 MET cc_start: 0.5787 (mpp) cc_final: 0.5073 (mmm) REVERT: F 143 LEU cc_start: 0.5815 (mt) cc_final: 0.5259 (tt) REVERT: G 99 PHE cc_start: 0.7171 (p90) cc_final: 0.6893 (p90) REVERT: G 192 GLN cc_start: 0.6146 (mp10) cc_final: 0.4979 (mp10) REVERT: G 204 ARG cc_start: 0.7391 (mmt180) cc_final: 0.6813 (mmt-90) REVERT: G 210 TRP cc_start: 0.6495 (t-100) cc_final: 0.6140 (t-100) REVERT: H 95 PHE cc_start: 0.6332 (m-80) cc_final: 0.5955 (m-80) REVERT: H 133 GLU cc_start: 0.7246 (mp0) cc_final: 0.6857 (mp0) REVERT: H 252 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6707 (mt-10) REVERT: I 78 LYS cc_start: 0.7488 (pttp) cc_final: 0.6161 (mttm) REVERT: I 248 MET cc_start: 0.8662 (mmm) cc_final: 0.8429 (tpp) REVERT: I 422 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6920 (tm-30) REVERT: J 29 LYS cc_start: 0.6583 (mttt) cc_final: 0.6188 (tttt) REVERT: J 49 GLU cc_start: 0.5829 (tp30) cc_final: 0.4383 (mm-30) REVERT: J 90 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6562 (tm-30) REVERT: J 91 GLU cc_start: 0.7079 (pm20) cc_final: 0.6621 (pm20) REVERT: J 104 LEU cc_start: 0.7500 (mp) cc_final: 0.7104 (tp) REVERT: J 172 LYS cc_start: 0.6154 (mtmm) cc_final: 0.5683 (tptp) REVERT: J 229 THR cc_start: 0.8468 (t) cc_final: 0.8267 (m) REVERT: J 237 LEU cc_start: 0.9359 (mt) cc_final: 0.9148 (mp) REVERT: J 299 ASP cc_start: 0.8058 (p0) cc_final: 0.7588 (p0) REVERT: J 442 LEU cc_start: 0.8178 (tp) cc_final: 0.7591 (tp) REVERT: K 186 VAL cc_start: 0.8123 (t) cc_final: 0.7892 (p) REVERT: K 187 TYR cc_start: 0.6462 (t80) cc_final: 0.6262 (t80) REVERT: K 259 MET cc_start: 0.8541 (mmm) cc_final: 0.8265 (mtt) REVERT: K 437 GLU cc_start: 0.3758 (mp0) cc_final: 0.2974 (mm-30) REVERT: N 324 MET cc_start: 0.2769 (mmm) cc_final: 0.2546 (mmm) REVERT: O 324 MET cc_start: 0.0124 (tpp) cc_final: -0.1254 (mtm) outliers start: 1 outliers final: 0 residues processed: 622 average time/residue: 0.2194 time to fit residues: 223.2802 Evaluate side-chains 494 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 296 optimal weight: 9.9990 chunk 423 optimal weight: 7.9990 chunk 393 optimal weight: 9.9990 chunk 91 optimal weight: 0.0030 chunk 36 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 422 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN E 147 HIS E 258 ASN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 GLN ** I 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.150259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114790 restraints weight = 61467.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112526 restraints weight = 44252.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112865 restraints weight = 41801.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113265 restraints weight = 36370.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113706 restraints weight = 29772.117| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35604 Z= 0.185 Angle : 0.701 14.043 48228 Z= 0.356 Chirality : 0.047 0.276 5233 Planarity : 0.006 0.085 6307 Dihedral : 5.376 28.327 4819 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.49 % Favored : 92.46 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.12), residues: 4350 helix: 0.47 (0.12), residues: 1754 sheet: -0.74 (0.19), residues: 636 loop : -2.02 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 131 TYR 0.026 0.002 TYR A 22 PHE 0.049 0.002 PHE J 266 TRP 0.018 0.002 TRP K 365 HIS 0.018 0.001 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00437 (35601) covalent geometry : angle 0.70082 (48224) SS BOND : bond 0.00642 ( 2) SS BOND : angle 2.06396 ( 4) hydrogen bonds : bond 0.03960 ( 1457) hydrogen bonds : angle 4.92436 ( 4152) Misc. bond : bond 0.00360 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 599 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ARG cc_start: 0.6798 (mmp-170) cc_final: 0.6507 (mmp-170) REVERT: A 224 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7782 (mttp) REVERT: A 279 LYS cc_start: 0.8184 (tptp) cc_final: 0.6795 (mmtt) REVERT: B 103 ASP cc_start: 0.7879 (m-30) cc_final: 0.7473 (m-30) REVERT: B 224 LYS cc_start: 0.7558 (tttt) cc_final: 0.7259 (mmtm) REVERT: B 302 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7248 (tpp80) REVERT: B 336 LYS cc_start: 0.6628 (pttt) cc_final: 0.5638 (ttpt) REVERT: B 385 PRO cc_start: 0.8941 (Cg_endo) cc_final: 0.8577 (Cg_exo) REVERT: B 440 ASP cc_start: 0.6531 (p0) cc_final: 0.6320 (m-30) REVERT: C 48 ASP cc_start: 0.7648 (m-30) cc_final: 0.7137 (m-30) REVERT: C 128 ARG cc_start: 0.6901 (tpp80) cc_final: 0.6602 (ttt-90) REVERT: C 457 ASP cc_start: 0.6863 (p0) cc_final: 0.6569 (m-30) REVERT: D 95 PHE cc_start: 0.7926 (m-80) cc_final: 0.7655 (m-80) REVERT: D 393 ASP cc_start: 0.7312 (m-30) cc_final: 0.6941 (m-30) REVERT: D 415 THR cc_start: 0.8548 (t) cc_final: 0.8259 (t) REVERT: D 435 TYR cc_start: 0.6133 (t80) cc_final: 0.5850 (t80) REVERT: E 91 LEU cc_start: 0.7599 (tp) cc_final: 0.7333 (tt) REVERT: E 99 PHE cc_start: 0.7586 (p90) cc_final: 0.7353 (p90) REVERT: E 120 GLU cc_start: 0.6279 (mt-10) cc_final: 0.5758 (mm-30) REVERT: E 179 THR cc_start: 0.8222 (p) cc_final: 0.7901 (t) REVERT: E 184 ARG cc_start: 0.6644 (mpt180) cc_final: 0.4644 (ttp80) REVERT: E 202 PRO cc_start: 0.6060 (Cg_endo) cc_final: 0.5791 (Cg_exo) REVERT: E 205 ARG cc_start: 0.7003 (mmt-90) cc_final: 0.6549 (mtp85) REVERT: E 208 VAL cc_start: 0.7594 (p) cc_final: 0.7357 (p) REVERT: E 228 ARG cc_start: 0.6721 (mmm-85) cc_final: 0.5321 (mmm-85) REVERT: F 70 PRO cc_start: 0.5158 (Cg_exo) cc_final: 0.4842 (Cg_endo) REVERT: F 95 MET cc_start: 0.5805 (mpp) cc_final: 0.5046 (mmm) REVERT: F 143 LEU cc_start: 0.5793 (mt) cc_final: 0.5225 (tt) REVERT: F 186 ILE cc_start: 0.5491 (tt) cc_final: 0.5235 (tp) REVERT: G 99 PHE cc_start: 0.7213 (p90) cc_final: 0.6910 (p90) REVERT: G 204 ARG cc_start: 0.7386 (mmt180) cc_final: 0.6887 (mmt180) REVERT: G 210 TRP cc_start: 0.6472 (t-100) cc_final: 0.6174 (t-100) REVERT: H 95 PHE cc_start: 0.6335 (m-80) cc_final: 0.5941 (m-80) REVERT: H 133 GLU cc_start: 0.7259 (mp0) cc_final: 0.6868 (mp0) REVERT: H 252 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6701 (mt-10) REVERT: I 78 LYS cc_start: 0.7500 (pttp) cc_final: 0.6158 (mttm) REVERT: I 117 ILE cc_start: 0.9066 (tp) cc_final: 0.8812 (tt) REVERT: I 315 LEU cc_start: 0.8233 (tt) cc_final: 0.8022 (tt) REVERT: I 363 GLN cc_start: 0.9067 (tp40) cc_final: 0.8482 (tp-100) REVERT: I 422 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6894 (tm-30) REVERT: J 29 LYS cc_start: 0.6628 (mttt) cc_final: 0.6285 (tttt) REVERT: J 49 GLU cc_start: 0.5868 (tp30) cc_final: 0.4394 (mm-30) REVERT: J 91 GLU cc_start: 0.7098 (pm20) cc_final: 0.6671 (pm20) REVERT: J 172 LYS cc_start: 0.6127 (mtmm) cc_final: 0.5700 (tptp) REVERT: J 229 THR cc_start: 0.8504 (t) cc_final: 0.8280 (m) REVERT: J 299 ASP cc_start: 0.8106 (p0) cc_final: 0.7645 (p0) REVERT: J 354 ASP cc_start: 0.6848 (t70) cc_final: 0.6493 (m-30) REVERT: J 442 LEU cc_start: 0.8235 (tp) cc_final: 0.7655 (tp) REVERT: K 186 VAL cc_start: 0.8183 (t) cc_final: 0.7931 (p) REVERT: K 187 TYR cc_start: 0.6462 (t80) cc_final: 0.6253 (t80) REVERT: K 259 MET cc_start: 0.8554 (mmm) cc_final: 0.8255 (mtt) REVERT: N 324 MET cc_start: 0.2850 (mmm) cc_final: 0.2623 (mmm) REVERT: O 324 MET cc_start: 0.0050 (tpp) cc_final: -0.1256 (mtm) outliers start: 1 outliers final: 1 residues processed: 600 average time/residue: 0.1957 time to fit residues: 194.0850 Evaluate side-chains 490 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 489 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 257 optimal weight: 0.9980 chunk 220 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 139 optimal weight: 0.0670 chunk 325 optimal weight: 5.9990 chunk 355 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 284 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN E 147 HIS E 246 GLN H 153 GLN H 383 HIS J 181 ASN ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 ASN ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119305 restraints weight = 60531.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118154 restraints weight = 38859.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117272 restraints weight = 40129.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117763 restraints weight = 35901.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117947 restraints weight = 31718.834| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35604 Z= 0.120 Angle : 0.642 12.191 48228 Z= 0.325 Chirality : 0.045 0.288 5233 Planarity : 0.006 0.095 6307 Dihedral : 5.030 28.065 4819 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.95 % Favored : 94.02 % Rotamer: Outliers : 0.03 % Allowed : 0.36 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.12), residues: 4350 helix: 0.73 (0.12), residues: 1765 sheet: -0.63 (0.19), residues: 654 loop : -1.95 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 428 TYR 0.022 0.001 TYR F 109 PHE 0.047 0.002 PHE I 266 TRP 0.013 0.001 TRP M 374 HIS 0.027 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00272 (35601) covalent geometry : angle 0.64224 (48224) SS BOND : bond 0.00352 ( 2) SS BOND : angle 1.64238 ( 4) hydrogen bonds : bond 0.03296 ( 1457) hydrogen bonds : angle 4.74441 ( 4152) Misc. bond : bond 0.00249 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7515.65 seconds wall clock time: 130 minutes 14.75 seconds (7814.75 seconds total)