Starting phenix.real_space_refine on Sun Jun 29 09:45:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ioj_35620/06_2025/8ioj_35620_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ioj_35620/06_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_35620/06_2025/8ioj_35620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ioj_35620/06_2025/8ioj_35620.map" model { file = "/net/cci-nas-00/data/ceres_data/8ioj_35620/06_2025/8ioj_35620_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ioj_35620/06_2025/8ioj_35620_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 3, 'ARG:plan': 1} 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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 21.77, per 1000 atoms: 0.63 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: 8.02 Conformation dependent library (CDL) restraints added in 4.8 seconds 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: 3.87 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: 12.46 Time building geometry restraints manager: 9.72 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: 4.470 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: 0.030 Extract box with map and model: 1.790 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 75.820 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.150 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.700 ------------------------------------------------------------------------------- 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 : 18.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.002 TRP J 382 HIS 0.007 0.001 HIS H 291 PHE 0.024 0.002 PHE I 266 TYR 0.015 0.002 TYR J 182 ARG 0.009 0.001 ARG K 316 Details of bonding type rmsd hydrogen bonds : bond 0.16011 ( 1457) hydrogen bonds : angle 7.22795 ( 4152) SS BOND : bond 0.00469 ( 2) SS BOND : angle 2.92134 ( 4) covalent geometry : bond 0.01367 (35601) covalent geometry : angle 1.03873 (48224) 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 : 4.136 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: 0.7439 (t0) REVERT: A 42 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8028 (tp40) REVERT: A 49 GLU cc_start: 0.7339 (tp30) cc_final: 0.6747 (tp30) REVERT: A 112 ASN cc_start: 0.7318 (t0) cc_final: 0.6985 (t0) REVERT: A 125 LYS cc_start: 0.7425 (pttt) cc_final: 0.7112 (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: 0.7511 (mmtt) REVERT: A 216 LEU cc_start: 0.8694 (mt) cc_final: 0.8476 (mt) REVERT: A 220 ASP cc_start: 0.7994 (t0) cc_final: 0.7608 (m-30) REVERT: A 283 ASP cc_start: 0.6869 (m-30) cc_final: 0.6377 (m-30) REVERT: A 304 HIS cc_start: 0.8358 (t-90) cc_final: 0.8114 (t-90) REVERT: A 315 LEU cc_start: 0.9210 (tt) cc_final: 0.8931 (tt) REVERT: A 426 GLN cc_start: 0.8131 (tt0) cc_final: 0.7683 (tt0) REVERT: A 452 LEU cc_start: 0.5825 (pt) cc_final: 0.5506 (tp) REVERT: B 34 LEU cc_start: 0.9112 (mm) cc_final: 0.8585 (mm) 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: 0.8689 (m-80) REVERT: B 172 LYS cc_start: 0.6360 (tttt) cc_final: 0.6026 (mmtt) REVERT: B 203 ILE cc_start: 0.7734 (mt) cc_final: 0.6981 (tt) REVERT: B 209 GLN cc_start: 0.8105 (mt0) cc_final: 0.7848 (mt0) REVERT: B 210 ARG cc_start: 0.5983 (mmt-90) cc_final: 0.5394 (mmt180) REVERT: B 224 LYS cc_start: 0.7570 (tttt) cc_final: 0.6931 (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: 0.8867 (tt) REVERT: B 297 VAL cc_start: 0.7942 (p) cc_final: 0.7741 (t) REVERT: B 302 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7308 (tpp80) REVERT: B 328 VAL cc_start: 0.7569 (t) cc_final: 0.7262 (p) REVERT: B 336 LYS cc_start: 0.5728 (pttt) cc_final: 0.4970 (ttpt) REVERT: B 350 HIS cc_start: 0.8074 (t-90) cc_final: 0.7769 (t-90) REVERT: B 390 ILE cc_start: 0.8726 (mm) cc_final: 0.8442 (pt) REVERT: B 417 ASN cc_start: 0.6362 (m110) cc_final: 0.5879 (m110) REVERT: C 90 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.6051 (tm-30) REVERT: C 120 ASN cc_start: 0.8618 (p0) cc_final: 0.8378 (p0) REVERT: C 128 ARG cc_start: 0.7066 (tpp80) cc_final: 0.6541 (ttt-90) REVERT: C 202 ASN cc_start: 0.7521 (p0) cc_final: 0.7283 (p0) REVERT: C 248 MET cc_start: 0.8763 (mmp) cc_final: 0.8547 (tpp) REVERT: C 390 ILE cc_start: 0.8726 (mm) cc_final: 0.8432 (mm) REVERT: C 428 ARG cc_start: 0.8890 (ttp-170) cc_final: 0.8597 (ttt-90) REVERT: C 432 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7137 (mtp85) REVERT: C 448 TRP cc_start: 0.5879 (m100) cc_final: 0.5641 (m100) 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: 0.7397 (m-80) REVERT: D 125 LYS cc_start: 0.6633 (pttt) cc_final: 0.5891 (tppt) REVERT: D 127 ILE cc_start: 0.8235 (mm) cc_final: 0.7988 (mt) REVERT: D 171 ILE cc_start: 0.8843 (tp) cc_final: 0.8576 (tt) REVERT: D 203 ILE cc_start: 0.6507 (mm) cc_final: 0.5833 (mm) REVERT: D 206 GLN cc_start: 0.6987 (mt0) cc_final: 0.6687 (mp10) REVERT: D 208 PHE cc_start: 0.7551 (p90) cc_final: 0.7053 (p90) REVERT: D 231 GLU cc_start: 0.6482 (mt-10) cc_final: 0.6248 (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: 0.6961 (mtp85) REVERT: D 359 VAL cc_start: 0.9239 (t) cc_final: 0.9031 (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: 0.6472 (t80) REVERT: E 82 LEU cc_start: 0.6440 (mp) cc_final: 0.6172 (mm) REVERT: E 89 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8108 (mt-10) REVERT: E 119 GLU cc_start: 0.6514 (tt0) cc_final: 0.6096 (tt0) REVERT: E 164 TYR cc_start: 0.7130 (t80) cc_final: 0.6817 (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: 0.4730 (ttp80) REVERT: E 205 ARG cc_start: 0.7291 (mmt-90) cc_final: 0.6992 (mtp85) REVERT: E 226 TYR cc_start: 0.6904 (m-10) cc_final: 0.6531 (m-80) REVERT: E 228 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.5416 (mmm160) REVERT: F 69 ARG cc_start: 0.4947 (OUTLIER) cc_final: 0.4382 (mtm180) REVERT: F 95 MET cc_start: 0.4844 (pmm) cc_final: 0.4303 (mpp) REVERT: G 68 PHE cc_start: 0.4898 (t80) cc_final: 0.4548 (t80) REVERT: G 117 THR cc_start: 0.7144 (p) cc_final: 0.6851 (t) REVERT: G 145 SER cc_start: 0.6383 (OUTLIER) cc_final: 0.5677 (m) REVERT: G 173 GLN cc_start: 0.7231 (mt0) cc_final: 0.6786 (mt0) REVERT: G 185 ASN cc_start: 0.7270 (t0) cc_final: 0.7033 (p0) REVERT: G 201 TYR cc_start: 0.6696 (t80) cc_final: 0.6013 (t80) REVERT: G 210 TRP cc_start: 0.6141 (t-100) cc_final: 0.5463 (t-100) REVERT: H 144 THR cc_start: 0.6279 (OUTLIER) cc_final: 0.5865 (t) REVERT: H 157 ASP cc_start: 0.7603 (m-30) cc_final: 0.6675 (m-30) REVERT: H 252 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7170 (mm-30) REVERT: H 339 THR cc_start: 0.8221 (m) cc_final: 0.7639 (t) REVERT: H 442 LEU cc_start: 0.5532 (OUTLIER) cc_final: 0.5269 (tp) REVERT: I 57 GLU cc_start: 0.5283 (tp30) cc_final: 0.4665 (tp30) REVERT: I 78 LYS cc_start: 0.6547 (pttp) cc_final: 0.5838 (mttm) REVERT: I 127 ILE cc_start: 0.7877 (mm) cc_final: 0.7168 (tp) REVERT: I 202 ASN cc_start: 0.7716 (p0) cc_final: 0.7000 (p0) REVERT: I 302 ARG cc_start: 0.6418 (ttm-80) cc_final: 0.6153 (tmm160) REVERT: I 307 HIS cc_start: 0.8591 (t-90) cc_final: 0.7992 (t-90) REVERT: I 315 LEU cc_start: 0.8550 (tt) cc_final: 0.7814 (tt) REVERT: I 336 LYS cc_start: 0.5070 (pttt) cc_final: 0.4283 (ptpp) REVERT: I 380 HIS cc_start: 0.6309 (p90) cc_final: 0.5733 (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: 0.5354 (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: 0.6968 (m-80) REVERT: J 95 PHE cc_start: 0.6966 (m-10) cc_final: 0.6386 (m-10) REVERT: J 107 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6788 (tt0) REVERT: J 210 ARG cc_start: 0.6617 (mmt180) cc_final: 0.6348 (mmt180) REVERT: J 224 LYS cc_start: 0.6421 (ttpt) cc_final: 0.6189 (mmmt) REVERT: J 255 LYS cc_start: 0.8598 (tmtt) cc_final: 0.8322 (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: 0.5954 (t80) REVERT: K 169 CYS cc_start: 0.7344 (t) cc_final: 0.6969 (p) REVERT: K 194 LEU cc_start: 0.7367 (mt) cc_final: 0.6863 (mt) REVERT: K 203 ILE cc_start: 0.6095 (mm) cc_final: 0.5841 (mt) REVERT: K 206 GLN cc_start: 0.7455 (mt0) cc_final: 0.6890 (mp10) REVERT: K 222 ILE cc_start: 0.8612 (mt) cc_final: 0.8200 (mm) REVERT: K 224 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7460 (tppt) REVERT: K 279 LYS cc_start: 0.7472 (mmmt) cc_final: 0.6927 (mtpt) REVERT: K 303 ASN cc_start: 0.7851 (m-40) cc_final: 0.7527 (m-40) REVERT: K 324 HIS cc_start: 0.7559 (m170) cc_final: 0.7040 (m-70) REVERT: K 328 VAL cc_start: 0.7750 (t) cc_final: 0.7320 (m) REVERT: L 431 VAL cc_start: 0.0156 (OUTLIER) cc_final: -0.0447 (m) REVERT: M 316 GLU cc_start: 0.3976 (OUTLIER) cc_final: 0.2985 (tt0) REVERT: M 342 LYS cc_start: 0.1205 (OUTLIER) cc_final: 0.0591 (mmtm) REVERT: M 343 ARG cc_start: 0.0957 (OUTLIER) cc_final: -0.0218 (mmm160) REVERT: N 292 ARG cc_start: -0.0231 (OUTLIER) cc_final: -0.0622 (ttp-110) REVERT: N 361 VAL cc_start: 0.4082 (OUTLIER) cc_final: 0.3661 (p) REVERT: N 379 GLU cc_start: -0.1404 (OUTLIER) cc_final: -0.2184 (mp0) REVERT: N 396 ASP cc_start: 0.3731 (OUTLIER) cc_final: 0.2872 (m-30) REVERT: N 402 VAL cc_start: -0.1784 (OUTLIER) cc_final: -0.2013 (p) REVERT: N 413 SER cc_start: 0.2787 (OUTLIER) cc_final: 0.2480 (t) REVERT: O 341 TRP cc_start: 0.2457 (t-100) cc_final: 0.1354 (t-100) REVERT: O 342 LYS cc_start: 0.4020 (OUTLIER) cc_final: 0.2939 (tptp) REVERT: O 426 MET cc_start: -0.1096 (ttt) cc_final: -0.1331 (tmm) outliers start: 222 outliers final: 46 residues processed: 1239 average time/residue: 0.5244 time to fit residues: 1005.9547 Evaluate side-chains 677 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 615 time to evaluate : 3.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 6.9990 chunk 333 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 344 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 399 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 324 HIS A 380 HIS A 383 HIS B 112 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 233 ASN E 246 GLN G 144 GLN G 173 GLN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN H 42 GLN ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 ASN ** I 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 GLN K 160 ASN K 284 ASN ** K 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.149893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114388 restraints weight = 61815.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113505 restraints weight = 60532.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114997 restraints weight = 41674.351| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 35604 Z= 0.296 Angle : 0.841 16.332 48228 Z= 0.437 Chirality : 0.052 0.248 5233 Planarity : 0.007 0.120 6307 Dihedral : 6.111 37.259 4819 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.89 % Favored : 92.02 % Rotamer: Outliers : 0.36 % Allowed : 7.40 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.12), residues: 4350 helix: -0.69 (0.12), residues: 1726 sheet: -1.89 (0.18), residues: 608 loop : -2.58 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP K 365 HIS 0.010 0.002 HIS J 324 PHE 0.047 0.003 PHE O 332 TYR 0.023 0.003 TYR I 236 ARG 0.011 0.001 ARG L 366 Details of bonding type rmsd hydrogen bonds : bond 0.04947 ( 1457) hydrogen bonds : angle 5.60436 ( 4152) SS BOND : bond 0.01964 ( 2) SS BOND : angle 2.22028 ( 4) covalent geometry : bond 0.00683 (35601) covalent geometry : angle 0.84043 (48224) Misc. bond : bond 0.00664 ( 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 755 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 742 time to evaluate : 7.841 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: 0.7547 (p0) cc_final: 0.7066 (t70) REVERT: A 49 GLU cc_start: 0.6202 (tp30) cc_final: 0.5919 (tp30) REVERT: A 125 LYS cc_start: 0.7255 (pttt) cc_final: 0.6872 (tttt) REVERT: A 172 LYS cc_start: 0.6777 (tptm) cc_final: 0.5168 (ptpt) REVERT: A 279 LYS cc_start: 0.7767 (tptp) cc_final: 0.6705 (mmtt) REVERT: B 103 ASP cc_start: 0.7782 (m-30) cc_final: 0.7471 (m-30) REVERT: B 122 PHE cc_start: 0.8566 (m-80) cc_final: 0.8269 (m-80) REVERT: B 153 GLN cc_start: 0.7819 (mp10) cc_final: 0.7526 (mp10) REVERT: B 203 ILE cc_start: 0.7861 (mt) cc_final: 0.7351 (tt) REVERT: B 208 PHE cc_start: 0.6355 (OUTLIER) cc_final: 0.5595 (m-80) REVERT: B 224 LYS cc_start: 0.7908 (tttt) cc_final: 0.7620 (mmtm) REVERT: B 261 ILE cc_start: 0.9264 (pt) cc_final: 0.8869 (tt) REVERT: B 302 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.7282 (tpp80) REVERT: B 336 LYS cc_start: 0.6258 (pttt) cc_final: 0.5294 (ttpt) REVERT: B 350 HIS cc_start: 0.7735 (t-90) cc_final: 0.7473 (t-90) REVERT: B 372 LEU cc_start: 0.8922 (mt) cc_final: 0.8709 (mt) REVERT: B 385 PRO cc_start: 0.9073 (Cg_endo) cc_final: 0.8792 (Cg_exo) REVERT: C 48 ASP cc_start: 0.7724 (m-30) cc_final: 0.7433 (m-30) REVERT: C 120 ASN cc_start: 0.8378 (p0) cc_final: 0.8121 (p0) REVERT: C 128 ARG cc_start: 0.6919 (tpp80) cc_final: 0.6455 (ttt-90) REVERT: C 155 GLU cc_start: 0.8227 (pp20) cc_final: 0.7906 (pp20) REVERT: C 276 THR cc_start: 0.9099 (m) cc_final: 0.8830 (t) REVERT: C 336 LYS cc_start: 0.6435 (mttt) cc_final: 0.5517 (mtmm) REVERT: C 432 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7625 (mtp85) REVERT: C 435 TYR cc_start: 0.3362 (t80) cc_final: 0.3129 (t80) REVERT: D 95 PHE cc_start: 0.8050 (m-80) cc_final: 0.7783 (m-80) REVERT: D 125 LYS cc_start: 0.6659 (pttt) cc_final: 0.6153 (tppt) REVERT: D 146 GLN cc_start: 0.8302 (tt0) cc_final: 0.8063 (tt0) REVERT: D 171 ILE cc_start: 0.8522 (tp) cc_final: 0.8282 (tt) REVERT: D 203 ILE cc_start: 0.6945 (mm) cc_final: 0.6739 (mm) REVERT: D 300 ARG cc_start: 0.6411 (tpt90) cc_final: 0.5893 (tpt170) REVERT: D 417 ASN cc_start: 0.8266 (m-40) cc_final: 0.7888 (m110) REVERT: D 456 LEU cc_start: 0.8132 (mt) cc_final: 0.7820 (tp) REVERT: E 99 PHE cc_start: 0.7539 (p90) cc_final: 0.7306 (p90) REVERT: E 119 GLU cc_start: 0.5994 (tt0) cc_final: 0.5307 (tm-30) REVERT: E 184 ARG cc_start: 0.6926 (mpt180) cc_final: 0.4891 (ttp80) REVERT: E 192 GLN cc_start: 0.7532 (tt0) cc_final: 0.7133 (tt0) REVERT: E 205 ARG cc_start: 0.6970 (mmt-90) cc_final: 0.6665 (mtp85) REVERT: E 228 ARG cc_start: 0.6717 (mmm-85) cc_final: 0.5451 (mmm160) REVERT: F 70 PRO cc_start: 0.5274 (Cg_exo) cc_final: 0.4911 (Cg_endo) REVERT: F 95 MET cc_start: 0.4836 (pmm) cc_final: 0.4512 (mpp) REVERT: F 118 ILE cc_start: 0.6359 (mm) cc_final: 0.6069 (mt) REVERT: F 143 LEU cc_start: 0.5640 (mt) cc_final: 0.5220 (tt) REVERT: G 68 PHE cc_start: 0.4424 (t80) cc_final: 0.4214 (t80) REVERT: G 117 THR cc_start: 0.7792 (p) cc_final: 0.7483 (t) REVERT: G 124 ILE cc_start: 0.7703 (tp) cc_final: 0.7372 (tp) REVERT: G 127 ILE cc_start: 0.8762 (tp) cc_final: 0.8558 (tt) REVERT: H 153 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7313 (tm-30) REVERT: H 252 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7021 (mm-30) REVERT: H 259 MET cc_start: 0.7583 (mmt) cc_final: 0.7318 (mmt) REVERT: I 49 GLU cc_start: 0.7121 (tt0) cc_final: 0.6778 (mm-30) REVERT: I 78 LYS cc_start: 0.7047 (pttp) cc_final: 0.6081 (mttt) REVERT: I 94 TYR cc_start: 0.7915 (m-80) cc_final: 0.7525 (m-80) REVERT: I 155 GLU cc_start: 0.7578 (tt0) cc_final: 0.7231 (tt0) REVERT: I 266 PHE cc_start: 0.8518 (p90) cc_final: 0.8270 (p90) REVERT: I 336 LYS cc_start: 0.4543 (pttt) cc_final: 0.3593 (ptpp) REVERT: I 380 HIS cc_start: 0.6055 (p90) cc_final: 0.5495 (p90) REVERT: I 412 PRO cc_start: 0.7919 (Cg_exo) cc_final: 0.7612 (Cg_endo) REVERT: J 22 TYR cc_start: 0.6838 (t80) cc_final: 0.6181 (t80) REVERT: J 29 LYS cc_start: 0.6351 (mttt) cc_final: 0.6018 (ttpt) REVERT: J 187 TYR cc_start: 0.7880 (t80) cc_final: 0.7596 (t80) REVERT: K 195 ASP cc_start: 0.7673 (m-30) cc_final: 0.7417 (m-30) REVERT: K 224 LYS cc_start: 0.7414 (mtpt) cc_final: 0.7184 (tppt) REVERT: K 302 ARG cc_start: 0.7112 (ptm160) cc_final: 0.6449 (ttm-80) REVERT: K 303 ASN cc_start: 0.7860 (m-40) cc_final: 0.7602 (m-40) REVERT: K 336 LYS cc_start: 0.5779 (pttt) cc_final: 0.4878 (ptpt) outliers start: 13 outliers final: 4 residues processed: 751 average time/residue: 0.6709 time to fit residues: 815.2921 Evaluate side-chains 536 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 531 time to evaluate : 4.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 212 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 383 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 415 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 340 optimal weight: 3.9990 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 383 HIS A 426 GLN B 264 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN H 112 ASN H 181 ASN ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 GLN I 380 HIS ** I 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 390 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.148609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112158 restraints weight = 62552.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110582 restraints weight = 44299.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110498 restraints weight = 34588.363| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 35604 Z= 0.268 Angle : 0.773 15.336 48228 Z= 0.399 Chirality : 0.049 0.252 5233 Planarity : 0.006 0.098 6307 Dihedral : 5.948 33.333 4819 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.79 % Favored : 92.16 % Rotamer: Outliers : 0.11 % Allowed : 5.94 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.12), residues: 4350 helix: -0.33 (0.12), residues: 1739 sheet: -1.65 (0.18), residues: 608 loop : -2.44 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP K 365 HIS 0.014 0.002 HIS I 295 PHE 0.039 0.003 PHE H 342 TYR 0.028 0.002 TYR I 236 ARG 0.012 0.001 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 1457) hydrogen bonds : angle 5.38722 ( 4152) SS BOND : bond 0.01189 ( 2) SS BOND : angle 2.25553 ( 4) covalent geometry : bond 0.00622 (35601) covalent geometry : angle 0.77313 (48224) Misc. bond : bond 0.00002 ( 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 712 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 708 time to evaluate : 4.539 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: A 25 ASP cc_start: 0.7628 (p0) cc_final: 0.7150 (t70) REVERT: A 42 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7177 (tp40) REVERT: A 184 ARG cc_start: 0.7009 (mmp-170) cc_final: 0.6700 (mmp-170) REVERT: A 224 LYS cc_start: 0.8237 (ttmm) cc_final: 0.7904 (mttp) REVERT: A 279 LYS cc_start: 0.8112 (tptp) cc_final: 0.6624 (mttt) REVERT: B 103 ASP cc_start: 0.7891 (m-30) cc_final: 0.7535 (m-30) REVERT: B 122 PHE cc_start: 0.8522 (m-80) cc_final: 0.8229 (m-80) REVERT: B 153 GLN cc_start: 0.7746 (mp10) cc_final: 0.7424 (mp10) REVERT: B 203 ILE cc_start: 0.7612 (mt) cc_final: 0.7227 (tt) REVERT: B 224 LYS cc_start: 0.7542 (tttt) cc_final: 0.7310 (mmtm) REVERT: B 261 ILE cc_start: 0.9119 (pt) cc_final: 0.8856 (tt) REVERT: B 302 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.7266 (tpp80) REVERT: B 336 LYS cc_start: 0.6318 (pttt) cc_final: 0.5396 (ttpt) REVERT: C 48 ASP cc_start: 0.7741 (m-30) cc_final: 0.7397 (m-30) REVERT: C 94 TYR cc_start: 0.8003 (m-80) cc_final: 0.7705 (m-80) REVERT: C 128 ARG cc_start: 0.6914 (tpp80) cc_final: 0.6386 (ttt-90) REVERT: C 155 GLU cc_start: 0.8245 (pp20) cc_final: 0.7976 (pp20) REVERT: C 432 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7657 (mtp85) REVERT: D 95 PHE cc_start: 0.8117 (m-80) cc_final: 0.7776 (m-80) REVERT: D 125 LYS cc_start: 0.6575 (pttt) cc_final: 0.6079 (tppt) REVERT: D 171 ILE cc_start: 0.8620 (tp) cc_final: 0.8368 (tt) REVERT: D 203 ILE cc_start: 0.6838 (mm) cc_final: 0.6577 (mm) REVERT: D 300 ARG cc_start: 0.6487 (tpt90) cc_final: 0.5995 (tpt170) REVERT: D 336 LYS cc_start: 0.5732 (tttt) cc_final: 0.5325 (ttpt) REVERT: D 363 GLN cc_start: 0.8726 (tp40) cc_final: 0.8432 (tp-100) REVERT: D 408 TRP cc_start: 0.5821 (m-10) cc_final: 0.5564 (m100) REVERT: E 184 ARG cc_start: 0.6669 (mpt180) cc_final: 0.4713 (ttp80) REVERT: E 205 ARG cc_start: 0.7064 (mmt-90) cc_final: 0.6776 (mtp85) REVERT: E 228 ARG cc_start: 0.6820 (mmm-85) cc_final: 0.5358 (mmm-85) REVERT: F 118 ILE cc_start: 0.6434 (mm) cc_final: 0.6172 (mt) REVERT: F 143 LEU cc_start: 0.6056 (mt) cc_final: 0.5371 (tt) REVERT: G 99 PHE cc_start: 0.7253 (p90) cc_final: 0.6983 (p90) REVERT: H 252 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6903 (mm-30) REVERT: H 339 THR cc_start: 0.7703 (p) cc_final: 0.7450 (t) REVERT: I 30 ASP cc_start: 0.7303 (t70) cc_final: 0.7031 (t0) REVERT: I 49 GLU cc_start: 0.7326 (tt0) cc_final: 0.6934 (mm-30) REVERT: I 78 LYS cc_start: 0.7306 (pttp) cc_final: 0.6166 (mttt) REVERT: I 336 LYS cc_start: 0.4485 (pttt) cc_final: 0.3453 (ptpp) REVERT: I 363 GLN cc_start: 0.9232 (tp40) cc_final: 0.8550 (tp40) REVERT: I 380 HIS cc_start: 0.6149 (p-80) cc_final: 0.5863 (p90) REVERT: J 29 LYS cc_start: 0.6511 (mttt) cc_final: 0.5968 (ttpt) REVERT: J 95 PHE cc_start: 0.6904 (m-10) cc_final: 0.6578 (m-10) REVERT: J 187 TYR cc_start: 0.8074 (t80) cc_final: 0.7834 (t80) REVERT: J 299 ASP cc_start: 0.8083 (p0) cc_final: 0.7480 (p0) REVERT: J 342 PHE cc_start: 0.7496 (p90) cc_final: 0.7291 (p90) REVERT: K 224 LYS cc_start: 0.7376 (mtpt) cc_final: 0.7003 (tppt) REVERT: K 302 ARG cc_start: 0.7229 (ptm160) cc_final: 0.6217 (mtt90) REVERT: K 303 ASN cc_start: 0.7791 (m-40) cc_final: 0.7442 (m-40) REVERT: K 336 LYS cc_start: 0.6127 (pttt) cc_final: 0.4970 (ptpp) REVERT: K 437 GLU cc_start: 0.4014 (mp0) cc_final: 0.3215 (mm-30) outliers start: 4 outliers final: 1 residues processed: 711 average time/residue: 0.6490 time to fit residues: 752.6614 Evaluate side-chains 503 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 502 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 146 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 399 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 292 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 357 optimal weight: 6.9990 chunk 351 optimal weight: 0.9980 chunk 243 optimal weight: 0.6980 chunk 346 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 209 GLN ** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 GLN E 130 ASN E 147 HIS E 246 GLN G 173 GLN H 204 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN ** I 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 HIS J 206 GLN ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 410 ASN ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 HIS ** K 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.150382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114410 restraints weight = 61340.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.113349 restraints weight = 49539.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114730 restraints weight = 36439.519| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35604 Z= 0.178 Angle : 0.677 14.026 48228 Z= 0.348 Chirality : 0.046 0.241 5233 Planarity : 0.006 0.067 6307 Dihedral : 5.578 29.557 4819 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.01 % Favored : 92.94 % Rotamer: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.12), residues: 4350 helix: 0.09 (0.12), residues: 1746 sheet: -1.48 (0.18), residues: 620 loop : -2.27 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP K 365 HIS 0.008 0.001 HIS E 147 PHE 0.041 0.002 PHE O 332 TYR 0.031 0.002 TYR H 77 ARG 0.010 0.001 ARG O 387 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 1457) hydrogen bonds : angle 5.09863 ( 4152) SS BOND : bond 0.00924 ( 2) SS BOND : angle 2.12633 ( 4) covalent geometry : bond 0.00413 (35601) covalent geometry : angle 0.67639 (48224) Misc. bond : bond 0.00046 ( 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 697 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 694 time to evaluate : 3.748 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 25 ASP cc_start: 0.7423 (p0) cc_final: 0.7042 (t70) REVERT: A 125 LYS cc_start: 0.6538 (tttt) cc_final: 0.6235 (ptpt) REVERT: A 184 ARG cc_start: 0.6904 (mmp-170) cc_final: 0.6617 (mmp-170) REVERT: A 224 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7806 (mttp) REVERT: A 279 LYS cc_start: 0.7597 (tptp) cc_final: 0.6760 (mmtt) REVERT: A 301 GLN cc_start: 0.8031 (tp40) cc_final: 0.7599 (tp40) REVERT: A 315 LEU cc_start: 0.8842 (tt) cc_final: 0.8597 (tt) REVERT: B 103 ASP cc_start: 0.7744 (m-30) cc_final: 0.7424 (m-30) REVERT: B 122 PHE cc_start: 0.8431 (m-80) cc_final: 0.8104 (m-80) REVERT: B 203 ILE cc_start: 0.7651 (mt) cc_final: 0.7350 (tt) REVERT: B 224 LYS cc_start: 0.7607 (tttt) cc_final: 0.7376 (mmtm) REVERT: B 261 ILE cc_start: 0.9095 (pt) cc_final: 0.8877 (tt) REVERT: B 302 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7189 (tpp80) REVERT: B 336 LYS cc_start: 0.6383 (pttt) cc_final: 0.5362 (ttmt) REVERT: B 385 PRO cc_start: 0.9011 (Cg_endo) cc_final: 0.8658 (Cg_exo) REVERT: C 48 ASP cc_start: 0.7667 (m-30) cc_final: 0.7269 (m-30) REVERT: C 128 ARG cc_start: 0.6845 (tpp80) cc_final: 0.6284 (ttt-90) REVERT: C 368 MET cc_start: 0.8327 (tpp) cc_final: 0.8071 (ttm) REVERT: D 32 ASP cc_start: 0.7978 (m-30) cc_final: 0.7333 (t0) REVERT: D 95 PHE cc_start: 0.8014 (m-80) cc_final: 0.7700 (m-80) REVERT: D 171 ILE cc_start: 0.8716 (tp) cc_final: 0.8425 (tt) REVERT: D 300 ARG cc_start: 0.6399 (tpt90) cc_final: 0.5976 (tpt170) REVERT: D 363 GLN cc_start: 0.8660 (tp40) cc_final: 0.8406 (tp-100) REVERT: D 415 THR cc_start: 0.8602 (t) cc_final: 0.8274 (t) REVERT: E 99 PHE cc_start: 0.7545 (p90) cc_final: 0.7288 (p90) REVERT: E 205 ARG cc_start: 0.6900 (mmt-90) cc_final: 0.6532 (mtp85) REVERT: E 228 ARG cc_start: 0.6769 (mmm-85) cc_final: 0.5350 (mmm-85) REVERT: F 118 ILE cc_start: 0.6547 (mm) cc_final: 0.6258 (mt) REVERT: F 143 LEU cc_start: 0.6025 (mt) cc_final: 0.5414 (tt) REVERT: F 186 ILE cc_start: 0.5499 (tt) cc_final: 0.5086 (tp) REVERT: G 99 PHE cc_start: 0.7192 (p90) cc_final: 0.6910 (p90) REVERT: H 128 ARG cc_start: 0.6892 (ttt180) cc_final: 0.6637 (tpt170) REVERT: H 133 GLU cc_start: 0.7212 (mp0) cc_final: 0.6953 (mp0) REVERT: H 252 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6763 (mt-10) REVERT: H 256 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7539 (tm-30) REVERT: I 30 ASP cc_start: 0.7209 (t70) cc_final: 0.6941 (t0) REVERT: I 78 LYS cc_start: 0.7360 (pttp) cc_final: 0.6255 (mttm) REVERT: I 155 GLU cc_start: 0.7575 (tt0) cc_final: 0.7284 (tt0) REVERT: I 336 LYS cc_start: 0.4559 (pttt) cc_final: 0.3535 (ptpp) REVERT: I 363 GLN cc_start: 0.8947 (tp40) cc_final: 0.8563 (tp-100) REVERT: I 412 PRO cc_start: 0.7779 (Cg_exo) cc_final: 0.7406 (Cg_endo) REVERT: J 29 LYS cc_start: 0.6561 (mttt) cc_final: 0.6014 (ttpt) REVERT: J 90 GLU cc_start: 0.6438 (tm-30) cc_final: 0.5836 (tm-30) REVERT: J 95 PHE cc_start: 0.6791 (m-10) cc_final: 0.6487 (m-10) REVERT: J 299 ASP cc_start: 0.8021 (p0) cc_final: 0.7406 (p0) REVERT: J 342 PHE cc_start: 0.7438 (p90) cc_final: 0.7238 (p90) REVERT: K 224 LYS cc_start: 0.7478 (mtpt) cc_final: 0.7078 (tppt) REVERT: K 302 ARG cc_start: 0.6962 (ptm160) cc_final: 0.6607 (mtm-85) REVERT: K 303 ASN cc_start: 0.7675 (m-40) cc_final: 0.7389 (m-40) REVERT: L 344 TRP cc_start: 0.5299 (m100) cc_final: 0.5042 (m100) outliers start: 3 outliers final: 1 residues processed: 697 average time/residue: 0.4842 time to fit residues: 540.8833 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 : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 152 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 434 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 430 optimal weight: 40.0000 chunk 92 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 383 optimal weight: 10.0000 chunk 378 optimal weight: 4.9990 chunk 222 optimal weight: 0.0030 overall best weight: 3.8796 ------------------------------------------------------------------------------- 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 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN A 264 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS ** C 398 GLN ** 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 324 HIS ** I 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 HIS J 206 GLN ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 HIS ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.149820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113352 restraints weight = 61454.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112387 restraints weight = 48662.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114233 restraints weight = 33951.768| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 35604 Z= 0.198 Angle : 0.695 14.111 48228 Z= 0.357 Chirality : 0.047 0.247 5233 Planarity : 0.006 0.069 6307 Dihedral : 5.566 30.981 4819 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.66 % Favored : 92.28 % Rotamer: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4350 helix: 0.18 (0.12), residues: 1746 sheet: -1.25 (0.18), residues: 624 loop : -2.20 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP K 365 HIS 0.007 0.001 HIS E 147 PHE 0.040 0.002 PHE O 332 TYR 0.027 0.002 TYR J 236 ARG 0.013 0.001 ARG K 316 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 1457) hydrogen bonds : angle 5.06800 ( 4152) SS BOND : bond 0.00749 ( 2) SS BOND : angle 2.37973 ( 4) covalent geometry : bond 0.00460 (35601) covalent geometry : angle 0.69500 (48224) Misc. bond : bond 0.00086 ( 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 649 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 647 time to evaluate : 3.463 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: 0.7553 (p0) cc_final: 0.7237 (t70) REVERT: A 125 LYS cc_start: 0.6652 (tttt) cc_final: 0.6198 (ptpt) REVERT: A 184 ARG cc_start: 0.6851 (mmp-170) cc_final: 0.6550 (mmp-170) REVERT: A 224 LYS cc_start: 0.8164 (ttmm) cc_final: 0.7837 (mttp) REVERT: A 315 LEU cc_start: 0.8877 (tt) cc_final: 0.8675 (tt) REVERT: B 103 ASP cc_start: 0.7825 (m-30) cc_final: 0.7493 (m-30) REVERT: B 224 LYS cc_start: 0.7566 (tttt) cc_final: 0.7272 (mmtm) REVERT: B 261 ILE cc_start: 0.9123 (pt) cc_final: 0.8857 (tt) REVERT: B 302 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7256 (tpp80) REVERT: B 336 LYS cc_start: 0.6436 (pttt) cc_final: 0.5544 (ttpt) REVERT: C 48 ASP cc_start: 0.7807 (m-30) cc_final: 0.7453 (m-30) REVERT: C 49 GLU cc_start: 0.7015 (tp30) cc_final: 0.6604 (mm-30) REVERT: C 128 ARG cc_start: 0.6836 (tpp80) cc_final: 0.6445 (ttt-90) REVERT: C 209 GLN cc_start: 0.6797 (tt0) cc_final: 0.6486 (tt0) REVERT: C 295 HIS cc_start: 0.7721 (p-80) cc_final: 0.7506 (p-80) REVERT: C 315 LEU cc_start: 0.8556 (tt) cc_final: 0.8232 (tt) REVERT: C 368 MET cc_start: 0.8364 (tpp) cc_final: 0.8064 (ttm) REVERT: D 171 ILE cc_start: 0.8704 (tp) cc_final: 0.8372 (tt) REVERT: D 415 THR cc_start: 0.8607 (t) cc_final: 0.8307 (t) REVERT: E 99 PHE cc_start: 0.7552 (p90) cc_final: 0.7308 (p90) REVERT: E 205 ARG cc_start: 0.6863 (mmt-90) cc_final: 0.6468 (mtp85) REVERT: E 228 ARG cc_start: 0.6679 (mmm-85) cc_final: 0.5262 (mmm-85) REVERT: F 95 MET cc_start: 0.5719 (mpp) cc_final: 0.4950 (mmm) REVERT: F 118 ILE cc_start: 0.6487 (mm) cc_final: 0.6214 (tt) REVERT: F 143 LEU cc_start: 0.5982 (mt) cc_final: 0.5394 (tt) REVERT: G 99 PHE cc_start: 0.7238 (p90) cc_final: 0.6933 (p90) REVERT: H 128 ARG cc_start: 0.6986 (ttt180) cc_final: 0.6572 (tpt170) REVERT: H 252 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6719 (mt-10) REVERT: H 451 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6738 (pm20) REVERT: I 30 ASP cc_start: 0.7182 (t70) cc_final: 0.6947 (t0) REVERT: I 78 LYS cc_start: 0.7419 (pttp) cc_final: 0.6223 (mttm) REVERT: I 155 GLU cc_start: 0.7603 (tt0) cc_final: 0.7322 (tt0) REVERT: I 248 MET cc_start: 0.8839 (mmm) cc_final: 0.8638 (mmp) REVERT: I 363 GLN cc_start: 0.9022 (tp40) cc_final: 0.8615 (tp-100) REVERT: I 412 PRO cc_start: 0.7694 (Cg_exo) cc_final: 0.7349 (Cg_endo) REVERT: J 29 LYS cc_start: 0.6515 (mttt) cc_final: 0.5995 (ttpt) REVERT: J 49 GLU cc_start: 0.5694 (tp30) cc_final: 0.4423 (mm-30) REVERT: J 91 GLU cc_start: 0.6807 (pm20) cc_final: 0.6532 (pm20) REVERT: J 172 LYS cc_start: 0.5938 (mtmm) cc_final: 0.5472 (tptp) REVERT: J 299 ASP cc_start: 0.8121 (p0) cc_final: 0.7628 (p0) REVERT: K 76 ARG cc_start: 0.5056 (mtm180) cc_final: 0.4849 (mtm180) REVERT: K 171 ILE cc_start: 0.8220 (mp) cc_final: 0.7999 (mp) REVERT: K 224 LYS cc_start: 0.7373 (mtpt) cc_final: 0.7149 (tppt) REVERT: K 302 ARG cc_start: 0.6952 (ptm160) cc_final: 0.6231 (mtt90) REVERT: K 365 TRP cc_start: 0.7380 (m100) cc_final: 0.6991 (m100) REVERT: K 368 MET cc_start: 0.8577 (ttm) cc_final: 0.8276 (mtp) REVERT: M 426 MET cc_start: 0.3136 (ppp) cc_final: 0.2927 (ppp) outliers start: 2 outliers final: 0 residues processed: 648 average time/residue: 0.6359 time to fit residues: 691.4615 Evaluate side-chains 474 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 7.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 77 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 292 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 311 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** 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** A 324 HIS B 112 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN C 153 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 147 HIS ** I 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.152321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117283 restraints weight = 61631.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114589 restraints weight = 42342.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115369 restraints weight = 35442.704| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5405 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= 0.139 Angle : 0.634 14.446 48228 Z= 0.324 Chirality : 0.045 0.216 5233 Planarity : 0.005 0.073 6307 Dihedral : 5.295 29.317 4819 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.64 % Favored : 93.31 % Rotamer: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.12), residues: 4350 helix: 0.42 (0.12), residues: 1755 sheet: -0.99 (0.19), residues: 628 loop : -2.10 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 365 HIS 0.011 0.001 HIS D 304 PHE 0.037 0.002 PHE H 342 TYR 0.019 0.001 TYR F 109 ARG 0.007 0.001 ARG M 387 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 1457) hydrogen bonds : angle 4.86544 ( 4152) SS BOND : bond 0.00467 ( 2) SS BOND : angle 2.11569 ( 4) covalent geometry : bond 0.00317 (35601) covalent geometry : angle 0.63390 (48224) Misc. bond : bond 0.00032 ( 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 687 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 686 time to evaluate : 11.695 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: 0.7537 (p0) cc_final: 0.7215 (t70) REVERT: A 125 LYS cc_start: 0.6600 (tttt) cc_final: 0.6161 (ptpt) REVERT: A 184 ARG cc_start: 0.6851 (mmp-170) cc_final: 0.6482 (mmp-170) REVERT: A 224 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7809 (mttp) REVERT: A 276 THR cc_start: 0.9099 (m) cc_final: 0.8869 (t) REVERT: A 315 LEU cc_start: 0.8857 (tt) cc_final: 0.8613 (tt) REVERT: B 103 ASP cc_start: 0.7911 (m-30) cc_final: 0.7547 (m-30) REVERT: B 224 LYS cc_start: 0.7531 (tttt) cc_final: 0.7223 (mmtm) REVERT: B 302 ARG cc_start: 0.7726 (ttm-80) cc_final: 0.6907 (tpp80) REVERT: B 336 LYS cc_start: 0.6416 (pttt) cc_final: 0.5509 (ttpt) REVERT: B 354 ASP cc_start: 0.5632 (t70) cc_final: 0.5069 (t0) REVERT: B 385 PRO cc_start: 0.8942 (Cg_endo) cc_final: 0.8516 (Cg_exo) REVERT: C 48 ASP cc_start: 0.7805 (m-30) cc_final: 0.7417 (m-30) REVERT: C 93 SER cc_start: 0.7850 (p) cc_final: 0.7541 (p) REVERT: C 128 ARG cc_start: 0.6828 (tpp80) cc_final: 0.6591 (ttt-90) REVERT: C 209 GLN cc_start: 0.6812 (tt0) cc_final: 0.6425 (tt0) REVERT: C 315 LEU cc_start: 0.8428 (tt) cc_final: 0.8040 (tt) REVERT: C 368 MET cc_start: 0.8253 (tpp) cc_final: 0.8014 (ttm) REVERT: D 129 SER cc_start: 0.8269 (p) cc_final: 0.7443 (m) REVERT: D 303 ASN cc_start: 0.8048 (m-40) cc_final: 0.7571 (t0) REVERT: D 393 ASP cc_start: 0.7363 (m-30) cc_final: 0.7043 (m-30) REVERT: D 415 THR cc_start: 0.8553 (t) cc_final: 0.8259 (t) REVERT: E 87 LYS cc_start: 0.7040 (mttt) cc_final: 0.6681 (mtmm) REVERT: E 99 PHE cc_start: 0.7569 (p90) cc_final: 0.7341 (p90) REVERT: E 179 THR cc_start: 0.8147 (p) cc_final: 0.7812 (t) REVERT: E 205 ARG cc_start: 0.6923 (mmt-90) cc_final: 0.6567 (mtp85) REVERT: E 228 ARG cc_start: 0.6716 (mmm-85) cc_final: 0.5289 (mmm-85) REVERT: F 95 MET cc_start: 0.5880 (mpp) cc_final: 0.5189 (mmm) REVERT: F 118 ILE cc_start: 0.6700 (mm) cc_final: 0.6471 (mt) REVERT: F 143 LEU cc_start: 0.6004 (mt) cc_final: 0.5471 (tt) REVERT: G 99 PHE cc_start: 0.7133 (p90) cc_final: 0.6878 (p90) REVERT: H 128 ARG cc_start: 0.7065 (ttt180) cc_final: 0.6575 (tpt170) REVERT: H 252 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6776 (mt-10) REVERT: I 78 LYS cc_start: 0.7384 (pttp) cc_final: 0.6169 (mttm) REVERT: I 259 MET cc_start: 0.9160 (mmm) cc_final: 0.8941 (mmm) REVERT: I 363 GLN cc_start: 0.9075 (tp40) cc_final: 0.8646 (tp-100) REVERT: I 412 PRO cc_start: 0.7581 (Cg_exo) cc_final: 0.7218 (Cg_endo) REVERT: J 29 LYS cc_start: 0.6449 (mttt) cc_final: 0.5965 (ttpt) REVERT: J 49 GLU cc_start: 0.5787 (tp30) cc_final: 0.4413 (mm-30) REVERT: J 95 PHE cc_start: 0.6798 (m-80) cc_final: 0.6250 (m-10) REVERT: J 172 LYS cc_start: 0.5934 (mtmm) cc_final: 0.5493 (tptp) REVERT: J 236 TYR cc_start: 0.8078 (m-80) cc_final: 0.7649 (m-80) REVERT: J 237 LEU cc_start: 0.9375 (mt) cc_final: 0.8839 (mt) REVERT: J 259 MET cc_start: 0.8127 (mmm) cc_final: 0.7903 (mtt) REVERT: K 171 ILE cc_start: 0.8221 (mp) cc_final: 0.8007 (mp) REVERT: K 186 VAL cc_start: 0.8091 (t) cc_final: 0.7845 (p) REVERT: K 224 LYS cc_start: 0.7464 (mtpt) cc_final: 0.7016 (tppt) REVERT: K 302 ARG cc_start: 0.6939 (ptm160) cc_final: 0.6679 (mtm-85) REVERT: K 316 ARG cc_start: 0.7148 (ptm-80) cc_final: 0.6893 (ptt-90) outliers start: 1 outliers final: 0 residues processed: 686 average time/residue: 0.5859 time to fit residues: 651.4742 Evaluate side-chains 515 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 360 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 419 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 302 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN E 137 GLN E 258 ASN G 173 GLN I 223 HIS I 295 HIS ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 380 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114328 restraints weight = 61543.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112400 restraints weight = 41899.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112631 restraints weight = 32122.240| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35604 Z= 0.204 Angle : 0.688 13.874 48228 Z= 0.353 Chirality : 0.047 0.294 5233 Planarity : 0.006 0.076 6307 Dihedral : 5.455 29.075 4819 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.63 % Favored : 92.30 % Rotamer: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.12), residues: 4350 helix: 0.36 (0.12), residues: 1746 sheet: -0.91 (0.19), residues: 628 loop : -2.10 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP K 365 HIS 0.010 0.001 HIS D 304 PHE 0.047 0.002 PHE O 332 TYR 0.024 0.002 TYR A 22 ARG 0.015 0.001 ARG J 128 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 1457) hydrogen bonds : angle 4.95233 ( 4152) SS BOND : bond 0.00646 ( 2) SS BOND : angle 2.12794 ( 4) covalent geometry : bond 0.00472 (35601) covalent geometry : angle 0.68766 (48224) Misc. bond : bond 0.00237 ( 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 623 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 622 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7502 (p0) cc_final: 0.7221 (t70) REVERT: A 125 LYS cc_start: 0.6726 (tttt) cc_final: 0.6201 (ptpt) REVERT: A 184 ARG cc_start: 0.6853 (mmp-170) cc_final: 0.6535 (mmp-170) REVERT: A 224 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7823 (mttp) REVERT: B 103 ASP cc_start: 0.7951 (m-30) cc_final: 0.7588 (m-30) REVERT: B 224 LYS cc_start: 0.7513 (tttt) cc_final: 0.7201 (mmtm) REVERT: B 302 ARG cc_start: 0.7646 (ttm-80) cc_final: 0.7047 (tpp80) REVERT: B 336 LYS cc_start: 0.6472 (pttt) cc_final: 0.5514 (ttpt) REVERT: B 440 ASP cc_start: 0.6643 (p0) cc_final: 0.6328 (m-30) REVERT: C 128 ARG cc_start: 0.6881 (tpp80) cc_final: 0.6414 (ttt-90) REVERT: C 129 SER cc_start: 0.7393 (p) cc_final: 0.7172 (p) REVERT: C 209 GLN cc_start: 0.6874 (tt0) cc_final: 0.6546 (tt0) REVERT: C 315 LEU cc_start: 0.8560 (tt) cc_final: 0.8193 (tt) REVERT: C 368 MET cc_start: 0.8373 (tpp) cc_final: 0.8142 (ttm) REVERT: D 206 GLN cc_start: 0.7949 (mp-120) cc_final: 0.7589 (mm-40) REVERT: D 300 ARG cc_start: 0.6365 (tpt90) cc_final: 0.6071 (tpt170) REVERT: D 415 THR cc_start: 0.8559 (t) cc_final: 0.8255 (t) REVERT: E 179 THR cc_start: 0.8159 (p) cc_final: 0.7816 (t) REVERT: E 202 PRO cc_start: 0.6146 (Cg_endo) cc_final: 0.5816 (Cg_exo) REVERT: E 205 ARG cc_start: 0.7038 (mmt-90) cc_final: 0.6629 (mtp85) REVERT: E 208 VAL cc_start: 0.7512 (p) cc_final: 0.7285 (p) REVERT: E 228 ARG cc_start: 0.6715 (mmm-85) cc_final: 0.5246 (mmm-85) REVERT: F 95 MET cc_start: 0.5894 (mpp) cc_final: 0.5279 (mmm) REVERT: F 118 ILE cc_start: 0.6606 (mm) cc_final: 0.6319 (tt) REVERT: F 143 LEU cc_start: 0.5978 (mt) cc_final: 0.5468 (tt) REVERT: F 186 ILE cc_start: 0.5391 (tt) cc_final: 0.5072 (tp) REVERT: G 99 PHE cc_start: 0.7232 (p90) cc_final: 0.6952 (p90) REVERT: H 252 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6765 (mt-10) REVERT: I 78 LYS cc_start: 0.7439 (pttp) cc_final: 0.6166 (mttm) REVERT: I 412 PRO cc_start: 0.7448 (Cg_exo) cc_final: 0.7120 (Cg_endo) REVERT: J 29 LYS cc_start: 0.6498 (mttt) cc_final: 0.5890 (ttpt) REVERT: J 49 GLU cc_start: 0.5819 (tp30) cc_final: 0.4384 (mm-30) REVERT: J 95 PHE cc_start: 0.6788 (m-80) cc_final: 0.6205 (m-10) REVERT: J 172 LYS cc_start: 0.6069 (mtmm) cc_final: 0.5511 (tptp) REVERT: J 236 TYR cc_start: 0.8207 (m-80) cc_final: 0.7808 (m-80) REVERT: J 237 LEU cc_start: 0.9404 (mt) cc_final: 0.8953 (mt) REVERT: K 186 VAL cc_start: 0.8126 (t) cc_final: 0.7894 (p) REVERT: K 224 LYS cc_start: 0.7433 (mtpt) cc_final: 0.6947 (tppt) REVERT: K 302 ARG cc_start: 0.6949 (ptm160) cc_final: 0.6331 (mtt90) REVERT: K 437 GLU cc_start: 0.3791 (mp0) cc_final: 0.3192 (mm-30) outliers start: 1 outliers final: 0 residues processed: 622 average time/residue: 0.4579 time to fit residues: 463.6659 Evaluate side-chains 473 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 24 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 428 optimal weight: 5.9990 chunk 266 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 393 optimal weight: 9.9990 chunk 315 optimal weight: 9.9990 chunk 324 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 264 optimal weight: 0.9990 chunk 169 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS B 112 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN C 380 HIS D 146 GLN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN E 258 ASN ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 398 GLN K 83 HIS ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114235 restraints weight = 61691.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111891 restraints weight = 43093.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112453 restraints weight = 35240.978| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 35604 Z= 0.196 Angle : 0.692 13.423 48228 Z= 0.355 Chirality : 0.047 0.274 5233 Planarity : 0.006 0.090 6307 Dihedral : 5.520 31.796 4819 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.66 % Favored : 92.32 % Rotamer: Outliers : 0.03 % Allowed : 1.66 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.12), residues: 4350 helix: 0.33 (0.12), residues: 1746 sheet: -0.82 (0.19), residues: 620 loop : -2.08 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP K 365 HIS 0.016 0.001 HIS C 295 PHE 0.043 0.002 PHE O 332 TYR 0.026 0.002 TYR H 77 ARG 0.009 0.001 ARG H 355 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 1457) hydrogen bonds : angle 4.99756 ( 4152) SS BOND : bond 0.00630 ( 2) SS BOND : angle 2.08471 ( 4) covalent geometry : bond 0.00459 (35601) covalent geometry : angle 0.69184 (48224) Misc. bond : bond 0.00398 ( 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 627 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 626 time to evaluate : 4.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7517 (p0) cc_final: 0.7194 (t70) REVERT: A 184 ARG cc_start: 0.6884 (mmp-170) cc_final: 0.6552 (mmp-170) REVERT: A 224 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7815 (mttp) REVERT: B 103 ASP cc_start: 0.7912 (m-30) cc_final: 0.7562 (m-30) REVERT: B 224 LYS cc_start: 0.7509 (tttt) cc_final: 0.7233 (mmtm) REVERT: B 302 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.6968 (tpp80) REVERT: B 336 LYS cc_start: 0.6514 (pttt) cc_final: 0.5643 (ttpt) REVERT: B 440 ASP cc_start: 0.6548 (p0) cc_final: 0.6187 (m-30) REVERT: C 128 ARG cc_start: 0.6850 (tpp80) cc_final: 0.6532 (ttt-90) REVERT: C 155 GLU cc_start: 0.8130 (pp20) cc_final: 0.7896 (pp20) REVERT: C 209 GLN cc_start: 0.6939 (tt0) cc_final: 0.6649 (tt0) REVERT: C 315 LEU cc_start: 0.8574 (tt) cc_final: 0.8222 (tt) REVERT: C 368 MET cc_start: 0.8372 (tpp) cc_final: 0.8083 (ttm) REVERT: D 204 ASN cc_start: 0.7764 (p0) cc_final: 0.7557 (p0) REVERT: D 206 GLN cc_start: 0.8008 (mp-120) cc_final: 0.7751 (mp10) REVERT: D 294 MET cc_start: 0.7766 (mtm) cc_final: 0.7565 (ttp) REVERT: D 415 THR cc_start: 0.8553 (t) cc_final: 0.8275 (t) REVERT: D 435 TYR cc_start: 0.6137 (t80) cc_final: 0.5861 (t80) REVERT: E 99 PHE cc_start: 0.7595 (p90) cc_final: 0.7370 (p90) REVERT: E 179 THR cc_start: 0.8163 (p) cc_final: 0.7832 (t) REVERT: E 184 ARG cc_start: 0.6681 (mpt180) cc_final: 0.5539 (tpp-160) REVERT: E 202 PRO cc_start: 0.6162 (Cg_endo) cc_final: 0.5843 (Cg_exo) REVERT: E 205 ARG cc_start: 0.6932 (mmt-90) cc_final: 0.6513 (mtp85) REVERT: E 228 ARG cc_start: 0.6708 (mmm-85) cc_final: 0.5224 (mmm-85) REVERT: F 95 MET cc_start: 0.5907 (mpp) cc_final: 0.5293 (mmm) REVERT: F 118 ILE cc_start: 0.6752 (mm) cc_final: 0.6524 (mt) REVERT: F 143 LEU cc_start: 0.5874 (mt) cc_final: 0.5358 (tt) REVERT: F 186 ILE cc_start: 0.5454 (tt) cc_final: 0.5139 (tp) REVERT: G 99 PHE cc_start: 0.7202 (p90) cc_final: 0.6921 (p90) REVERT: H 252 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6782 (mt-10) REVERT: I 78 LYS cc_start: 0.7437 (pttp) cc_final: 0.6162 (mttm) REVERT: I 248 MET cc_start: 0.8502 (mmp) cc_final: 0.8262 (mmp) REVERT: J 29 LYS cc_start: 0.6520 (mttt) cc_final: 0.6160 (tttt) REVERT: J 49 GLU cc_start: 0.5982 (tp30) cc_final: 0.4506 (mm-30) REVERT: J 95 PHE cc_start: 0.6786 (m-80) cc_final: 0.6147 (m-10) REVERT: J 172 LYS cc_start: 0.6088 (mtmm) cc_final: 0.5564 (tptp) REVERT: J 236 TYR cc_start: 0.8113 (m-80) cc_final: 0.7854 (m-80) REVERT: K 186 VAL cc_start: 0.8157 (t) cc_final: 0.7926 (p) REVERT: K 224 LYS cc_start: 0.7359 (mtpt) cc_final: 0.7081 (tppt) REVERT: K 259 MET cc_start: 0.8564 (mmm) cc_final: 0.8291 (mtt) REVERT: K 288 LEU cc_start: 0.9323 (tp) cc_final: 0.8911 (tt) REVERT: K 302 ARG cc_start: 0.6907 (ptm160) cc_final: 0.6354 (mtt90) REVERT: K 437 GLU cc_start: 0.3875 (mp0) cc_final: 0.3244 (mm-30) REVERT: O 324 MET cc_start: -0.0131 (tpp) cc_final: -0.1373 (mtm) outliers start: 1 outliers final: 0 residues processed: 626 average time/residue: 0.4839 time to fit residues: 493.3845 Evaluate side-chains 487 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 3.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 304 optimal weight: 3.9990 chunk 429 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 355 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 304 HIS B 322 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN E 258 ASN ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** 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 = 0.3829 r_free = 0.3829 target = 0.150359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112124 restraints weight = 61460.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111726 restraints weight = 36899.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112297 restraints weight = 33385.859| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35604 Z= 0.182 Angle : 0.685 12.943 48228 Z= 0.352 Chirality : 0.047 0.297 5233 Planarity : 0.006 0.085 6307 Dihedral : 5.439 35.907 4819 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.66 % Favored : 92.32 % Rotamer: Outliers : 0.03 % Allowed : 1.08 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.12), residues: 4350 helix: 0.34 (0.12), residues: 1758 sheet: -0.75 (0.19), residues: 616 loop : -2.07 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP K 365 HIS 0.012 0.001 HIS D 304 PHE 0.044 0.002 PHE O 332 TYR 0.032 0.002 TYR H 77 ARG 0.008 0.001 ARG H 357 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 1457) hydrogen bonds : angle 4.94877 ( 4152) SS BOND : bond 0.00623 ( 2) SS BOND : angle 2.03018 ( 4) covalent geometry : bond 0.00424 (35601) covalent geometry : angle 0.68479 (48224) Misc. bond : bond 0.00101 ( 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 610 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 609 time to evaluate : 3.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7488 (p0) cc_final: 0.7210 (t70) REVERT: A 184 ARG cc_start: 0.6853 (mmp-170) cc_final: 0.6503 (mmp-170) REVERT: A 224 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7815 (mttp) REVERT: A 315 LEU cc_start: 0.8824 (tt) cc_final: 0.8603 (tt) REVERT: B 103 ASP cc_start: 0.7853 (m-30) cc_final: 0.7523 (m-30) REVERT: B 224 LYS cc_start: 0.7526 (tttt) cc_final: 0.7226 (mmtm) REVERT: B 302 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.6969 (tpp80) REVERT: B 336 LYS cc_start: 0.6466 (pttt) cc_final: 0.5524 (ttpt) REVERT: C 128 ARG cc_start: 0.6885 (tpp80) cc_final: 0.6538 (ttt-90) REVERT: C 209 GLN cc_start: 0.7001 (tt0) cc_final: 0.6699 (tt0) REVERT: C 295 HIS cc_start: 0.6860 (p-80) cc_final: 0.6361 (p-80) REVERT: C 315 LEU cc_start: 0.8729 (tt) cc_final: 0.8328 (tt) REVERT: C 368 MET cc_start: 0.8365 (tpp) cc_final: 0.8125 (ttm) REVERT: C 457 ASP cc_start: 0.6862 (p0) cc_final: 0.6530 (m-30) REVERT: D 160 ASN cc_start: 0.8196 (m-40) cc_final: 0.7827 (m110) REVERT: D 415 THR cc_start: 0.8515 (t) cc_final: 0.8219 (t) REVERT: D 417 ASN cc_start: 0.8193 (m-40) cc_final: 0.7987 (m110) REVERT: D 435 TYR cc_start: 0.6098 (t80) cc_final: 0.5819 (t80) REVERT: E 99 PHE cc_start: 0.7611 (p90) cc_final: 0.7410 (p90) REVERT: E 179 THR cc_start: 0.8143 (p) cc_final: 0.7793 (t) REVERT: E 202 PRO cc_start: 0.6065 (Cg_endo) cc_final: 0.5779 (Cg_exo) REVERT: E 205 ARG cc_start: 0.6951 (mmt-90) cc_final: 0.6501 (mtp85) REVERT: E 208 VAL cc_start: 0.7609 (p) cc_final: 0.7401 (p) REVERT: E 228 ARG cc_start: 0.6711 (mmm-85) cc_final: 0.5230 (mmm-85) REVERT: F 95 MET cc_start: 0.5998 (mpp) cc_final: 0.5423 (mmm) REVERT: F 118 ILE cc_start: 0.6714 (mm) cc_final: 0.6422 (mt) REVERT: F 143 LEU cc_start: 0.5904 (mt) cc_final: 0.5413 (tt) REVERT: F 186 ILE cc_start: 0.5305 (tt) cc_final: 0.4943 (tp) REVERT: G 99 PHE cc_start: 0.7191 (p90) cc_final: 0.6933 (p90) REVERT: H 133 GLU cc_start: 0.7274 (mp0) cc_final: 0.6918 (mp0) REVERT: I 78 LYS cc_start: 0.7480 (pttp) cc_final: 0.6173 (mttm) REVERT: I 94 TYR cc_start: 0.7798 (m-80) cc_final: 0.7512 (m-80) REVERT: I 363 GLN cc_start: 0.9121 (tp40) cc_final: 0.8651 (tp40) REVERT: J 29 LYS cc_start: 0.6500 (mttt) cc_final: 0.6116 (tttt) REVERT: J 49 GLU cc_start: 0.5988 (tp30) cc_final: 0.4507 (mm-30) REVERT: J 95 PHE cc_start: 0.6814 (m-80) cc_final: 0.6157 (m-10) REVERT: J 172 LYS cc_start: 0.6033 (mtmm) cc_final: 0.5492 (tptp) REVERT: J 354 ASP cc_start: 0.6874 (t70) cc_final: 0.6467 (m-30) REVERT: J 442 LEU cc_start: 0.8262 (tp) cc_final: 0.7736 (tp) REVERT: K 186 VAL cc_start: 0.8149 (t) cc_final: 0.7941 (p) REVERT: K 259 MET cc_start: 0.8578 (mmm) cc_final: 0.8291 (mtt) REVERT: K 288 LEU cc_start: 0.9323 (tp) cc_final: 0.8915 (tt) REVERT: K 302 ARG cc_start: 0.6867 (ptm160) cc_final: 0.6251 (mtt90) REVERT: K 437 GLU cc_start: 0.3842 (mp0) cc_final: 0.3214 (mm-30) outliers start: 1 outliers final: 0 residues processed: 609 average time/residue: 0.4913 time to fit residues: 491.9602 Evaluate side-chains 481 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 9 optimal weight: 6.9990 chunk 350 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 396 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 384 optimal weight: 1.9990 chunk 412 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 209 GLN ** 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** J 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115350 restraints weight = 60977.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115298 restraints weight = 37591.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115547 restraints weight = 28135.296| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35604 Z= 0.137 Angle : 0.652 11.330 48228 Z= 0.334 Chirality : 0.046 0.288 5233 Planarity : 0.006 0.082 6307 Dihedral : 5.190 35.675 4819 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.60 % Favored : 93.38 % Rotamer: Outliers : 0.03 % Allowed : 0.19 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.12), residues: 4350 helix: 0.59 (0.13), residues: 1758 sheet: -0.61 (0.19), residues: 620 loop : -1.99 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 365 HIS 0.011 0.001 HIS C 295 PHE 0.036 0.002 PHE O 332 TYR 0.024 0.002 TYR K 22 ARG 0.016 0.000 ARG K 316 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 1457) hydrogen bonds : angle 4.81697 ( 4152) SS BOND : bond 0.00462 ( 2) SS BOND : angle 1.77884 ( 4) covalent geometry : bond 0.00316 (35601) covalent geometry : angle 0.65179 (48224) Misc. bond : bond 0.00257 ( 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 621 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 620 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ARG cc_start: 0.6809 (mmp-170) cc_final: 0.6479 (mmp-170) REVERT: A 224 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7779 (mttp) REVERT: A 395 SER cc_start: 0.9353 (m) cc_final: 0.9088 (t) REVERT: B 103 ASP cc_start: 0.7805 (m-30) cc_final: 0.7468 (m-30) REVERT: B 224 LYS cc_start: 0.7517 (tttt) cc_final: 0.7228 (mmtm) REVERT: B 302 ARG cc_start: 0.7643 (ttm-80) cc_final: 0.6805 (tpp80) REVERT: B 336 LYS cc_start: 0.6480 (pttt) cc_final: 0.5591 (ttpt) REVERT: B 440 ASP cc_start: 0.6499 (p0) cc_final: 0.6191 (m-30) REVERT: C 128 ARG cc_start: 0.6725 (tpp80) cc_final: 0.6483 (ttt-90) REVERT: C 209 GLN cc_start: 0.6918 (tt0) cc_final: 0.6599 (tt0) REVERT: C 315 LEU cc_start: 0.8474 (tt) cc_final: 0.8099 (tt) REVERT: C 368 MET cc_start: 0.8211 (tpp) cc_final: 0.7926 (ttm) REVERT: C 457 ASP cc_start: 0.6839 (p0) cc_final: 0.6588 (m-30) REVERT: D 303 ASN cc_start: 0.8195 (m-40) cc_final: 0.7686 (t0) REVERT: D 390 ILE cc_start: 0.8641 (pt) cc_final: 0.8202 (mm) REVERT: D 415 THR cc_start: 0.8425 (t) cc_final: 0.8115 (t) REVERT: D 435 TYR cc_start: 0.6054 (t80) cc_final: 0.5761 (t80) REVERT: E 99 PHE cc_start: 0.7610 (p90) cc_final: 0.7395 (p90) REVERT: E 179 THR cc_start: 0.8125 (p) cc_final: 0.7809 (t) REVERT: E 180 PHE cc_start: 0.7852 (t80) cc_final: 0.7236 (t80) REVERT: E 184 ARG cc_start: 0.6756 (mpt180) cc_final: 0.4545 (ttp80) REVERT: E 202 PRO cc_start: 0.5936 (Cg_endo) cc_final: 0.5681 (Cg_exo) REVERT: E 205 ARG cc_start: 0.6929 (mmt-90) cc_final: 0.6475 (mtp85) REVERT: E 228 ARG cc_start: 0.6754 (mmm-85) cc_final: 0.5323 (mmm-85) REVERT: F 95 MET cc_start: 0.5972 (mpp) cc_final: 0.5459 (mmm) REVERT: F 118 ILE cc_start: 0.6678 (mm) cc_final: 0.6382 (tt) REVERT: F 143 LEU cc_start: 0.5836 (mt) cc_final: 0.5365 (tt) REVERT: F 186 ILE cc_start: 0.5374 (tt) cc_final: 0.5050 (tp) REVERT: G 99 PHE cc_start: 0.7118 (p90) cc_final: 0.6883 (p90) REVERT: G 210 TRP cc_start: 0.6375 (t60) cc_final: 0.6116 (t60) REVERT: H 133 GLU cc_start: 0.7289 (mp0) cc_final: 0.6929 (mp0) REVERT: H 252 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6744 (mt-10) REVERT: I 78 LYS cc_start: 0.7435 (pttp) cc_final: 0.6162 (mttm) REVERT: I 94 TYR cc_start: 0.7724 (m-80) cc_final: 0.7446 (m-80) REVERT: J 29 LYS cc_start: 0.6472 (mttt) cc_final: 0.6173 (tttt) REVERT: J 49 GLU cc_start: 0.6016 (tp30) cc_final: 0.4491 (mm-30) REVERT: J 95 PHE cc_start: 0.6863 (m-80) cc_final: 0.6089 (m-10) REVERT: J 102 LEU cc_start: 0.8704 (tt) cc_final: 0.8362 (tp) REVERT: J 172 LYS cc_start: 0.6032 (mtmm) cc_final: 0.5505 (tptp) REVERT: J 237 LEU cc_start: 0.9375 (mt) cc_final: 0.9115 (mt) REVERT: J 442 LEU cc_start: 0.8232 (tp) cc_final: 0.7581 (tp) REVERT: K 186 VAL cc_start: 0.8157 (t) cc_final: 0.7909 (p) REVERT: K 259 MET cc_start: 0.8543 (mmm) cc_final: 0.8254 (mtt) REVERT: K 288 LEU cc_start: 0.9300 (tp) cc_final: 0.8923 (tt) REVERT: K 302 ARG cc_start: 0.6804 (ptm160) cc_final: 0.6245 (mtt90) REVERT: K 437 GLU cc_start: 0.3790 (mp0) cc_final: 0.3175 (mm-30) REVERT: L 420 VAL cc_start: 0.3885 (m) cc_final: 0.3511 (p) outliers start: 1 outliers final: 0 residues processed: 620 average time/residue: 0.4650 time to fit residues: 474.4101 Evaluate side-chains 499 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 12 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 431 optimal weight: 7.9990 chunk 202 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 259 optimal weight: 0.9980 chunk 374 optimal weight: 8.9990 chunk 345 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 112 ASN ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 258 ASN G 144 GLN G 233 ASN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 291 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** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 322 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 = 0.3800 r_free = 0.3800 target = 0.147935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112944 restraints weight = 62649.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111767 restraints weight = 55916.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113582 restraints weight = 41690.929| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 35604 Z= 0.263 Angle : 0.781 13.295 48228 Z= 0.402 Chirality : 0.050 0.294 5233 Planarity : 0.007 0.195 6307 Dihedral : 5.732 34.940 4819 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.44 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.12), residues: 4350 helix: 0.16 (0.12), residues: 1750 sheet: -0.71 (0.19), residues: 612 loop : -2.03 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 365 HIS 0.010 0.002 HIS I 235 PHE 0.043 0.003 PHE I 266 TYR 0.028 0.002 TYR A 22 ARG 0.011 0.001 ARG K 316 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 1457) hydrogen bonds : angle 5.15663 ( 4152) SS BOND : bond 0.00779 ( 2) SS BOND : angle 2.25334 ( 4) covalent geometry : bond 0.00618 (35601) covalent geometry : angle 0.78123 (48224) Misc. bond : bond 0.00169 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18019.93 seconds wall clock time: 319 minutes 15.15 seconds (19155.15 seconds total)