Starting phenix.real_space_refine on Thu Mar 5 10:52:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nho_12335/03_2026/7nho_12335.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nho_12335/03_2026/7nho_12335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nho_12335/03_2026/7nho_12335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nho_12335/03_2026/7nho_12335.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nho_12335/03_2026/7nho_12335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nho_12335/03_2026/7nho_12335.map" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 9 Type Number sf(0) Gaussians Mn 1 7.51 5 Fe 2 7.16 5 P 2 5.49 5 Mg 35 5.21 5 S 66 5.16 5 Cl 1 4.86 5 C 13764 2.51 5 N 2832 2.21 5 O 3097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19800 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2627 Classifications: {'peptide': 335} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 319} Chain: "B" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3812 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 31, 'TRANS': 453} Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3465 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 24, 'TRANS': 423} Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2705 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain: "E" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 635 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "F" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "H" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 511 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "I" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 286 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "K" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 293 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "L" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 304 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "M" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "T" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 256 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "X" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 254 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "y" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 208 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "Z" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 479 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "A" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 469 Unusual residues: {' CL': 1, ' FE': 1, ' MN': 1, 'BCR': 1, 'BCT': 1, 'CLA': 4, 'LHG': 2, 'PHO': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1215 Unusual residues: {'BCR': 3, 'CLA': 16, 'LMG': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 980 Unusual residues: {'BCR': 2, 'CLA': 13, 'LMG': 1} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 414 Unusual residues: {'CLA': 2, 'LMG': 3, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.08, per 1000 atoms: 0.21 Number of scatterers: 19800 At special positions: 0 Unit cell: (111.18, 107.91, 136.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Fe 2 26.01 Mn 1 24.99 Cl 1 17.00 S 66 16.00 P 2 15.00 Mg 35 11.99 O 3097 8.00 N 2832 7.00 C 13764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 524.0 milliseconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3764 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 8 sheets defined 63.1% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 33 through 55 Proline residue: A 39 - end of helix removed outlier: 3.822A pdb=" N ILE A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 108 Processing helix chain 'A' and resid 109 through 137 removed outlier: 4.163A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N HIS A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP A 131 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.807A pdb=" N ALA A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.794A pdb=" N ASP A 170 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 171 " --> pdb=" O PHE A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 171' Processing helix chain 'A' and resid 175 through 191 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 221 removed outlier: 3.528A pdb=" N GLN A 199 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.721A pdb=" N TYR A 235 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 237 " --> pdb=" O ASN A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 237' Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.665A pdb=" N ALA A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 316 through 332 Processing helix chain 'B' and resid 15 through 43 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.938A pdb=" N MET B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 removed outlier: 3.671A pdb=" N ILE B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 219 removed outlier: 4.298A pdb=" N VAL B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 206 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 234 through 258 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.504A pdb=" N GLN B 274 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.604A pdb=" N GLU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.557A pdb=" N ASP B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 424 removed outlier: 3.599A pdb=" N VAL B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.867A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 31 removed outlier: 6.039A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 61 removed outlier: 3.846A pdb=" N GLY C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.530A pdb=" N GLU C 71 " --> pdb=" O PRO C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.832A pdb=" N ILE C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 removed outlier: 3.694A pdb=" N PHE C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 169 removed outlier: 3.601A pdb=" N MET C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 removed outlier: 3.725A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.639A pdb=" N VAL C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 257 through 281 Processing helix chain 'C' and resid 293 through 311 removed outlier: 3.616A pdb=" N ALA C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.532A pdb=" N ASN C 370 " --> pdb=" O ASN C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.533A pdb=" N GLU C 377 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 442 removed outlier: 3.625A pdb=" N TRP C 413 " --> pdb=" O SER C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'D' and resid 14 through 23 Processing helix chain 'D' and resid 30 through 55 removed outlier: 4.019A pdb=" N ILE D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix removed outlier: 3.669A pdb=" N THR D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.506A pdb=" N MET D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 107 removed outlier: 3.528A pdb=" N TRP D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 137 removed outlier: 3.998A pdb=" N THR D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 146 removed outlier: 3.566A pdb=" N ILE D 144 " --> pdb=" O PRO D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 157 removed outlier: 4.067A pdb=" N ILE D 150 " --> pdb=" O PHE D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 170 removed outlier: 4.066A pdb=" N PHE D 169 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 190 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 194 through 220 removed outlier: 3.576A pdb=" N ALA D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 257 removed outlier: 3.620A pdb=" N GLN D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 290 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 334 removed outlier: 3.544A pdb=" N LYS D 317 " --> pdb=" O THR D 313 " (cutoff:3.500A) Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'E' and resid 9 through 15 removed outlier: 3.847A pdb=" N ILE E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 40 removed outlier: 3.706A pdb=" N TRP E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Proline residue: E 28 - end of helix removed outlier: 3.947A pdb=" N VAL E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 71 through 82 Processing helix chain 'F' and resid 17 through 25 removed outlier: 4.177A pdb=" N VAL F 21 " --> pdb=" O THR F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 41 removed outlier: 3.502A pdb=" N ALA F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 12 Processing helix chain 'H' and resid 13 through 15 No H-bonds generated for 'chain 'H' and resid 13 through 15' Processing helix chain 'H' and resid 27 through 50 removed outlier: 4.236A pdb=" N VAL H 33 " --> pdb=" O PRO H 29 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 25 removed outlier: 3.630A pdb=" N ILE I 6 " --> pdb=" O GLU I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 30 removed outlier: 3.767A pdb=" N ALA I 29 " --> pdb=" O GLY I 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 17 removed outlier: 4.210A pdb=" N ILE K 17 " --> pdb=" O ALA K 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 14 through 17' Processing helix chain 'K' and resid 18 through 24 removed outlier: 3.501A pdb=" N VAL K 24 " --> pdb=" O PRO K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 43 removed outlier: 3.899A pdb=" N LEU K 31 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 36 removed outlier: 4.583A pdb=" N SER L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 31 removed outlier: 3.677A pdb=" N ILE M 9 " --> pdb=" O GLN M 5 " (cutoff:3.500A) Proline residue: M 18 - end of helix removed outlier: 3.689A pdb=" N THR M 29 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU M 30 " --> pdb=" O TYR M 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'X' and resid 4 through 35 removed outlier: 3.701A pdb=" N ASP X 35 " --> pdb=" O ILE X 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 21 through 40 removed outlier: 4.211A pdb=" N ILE y 25 " --> pdb=" O GLN y 21 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY y 29 " --> pdb=" O ILE y 25 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE y 30 " --> pdb=" O ALA y 26 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY y 32 " --> pdb=" O ILE y 28 " (cutoff:3.500A) Proline residue: y 33 - end of helix removed outlier: 3.924A pdb=" N ILE y 36 " --> pdb=" O GLY y 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 29 Proline residue: Z 24 - end of helix removed outlier: 3.506A pdb=" N SER Z 29 " --> pdb=" O VAL Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 57 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 307 removed outlier: 4.481A pdb=" N VAL A 306 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 166 through 169 Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.339A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.339A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLU B 431 " --> pdb=" O GLN B 338 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TRP B 340 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE B 429 " --> pdb=" O TRP B 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA8, first strand: chain 'C' and resid 358 through 359 removed outlier: 4.024A pdb=" N GLY C 362 " --> pdb=" O GLY C 359 " (cutoff:3.500A) 887 hydrogen bonds defined for protein. 2565 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.36: 5641 1.36 - 1.56: 14363 1.56 - 1.76: 356 1.76 - 1.95: 118 1.95 - 2.15: 144 Bond restraints: 20622 Sorted by residual: bond pdb=" CAD CLA C 512 " pdb=" CBD CLA C 512 " ideal model delta sigma weight residual 1.563 1.687 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C3D CLA B 615 " pdb=" CAD CLA B 615 " ideal model delta sigma weight residual 1.454 1.577 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" CAD CLA B 603 " pdb=" CBD CLA B 603 " ideal model delta sigma weight residual 1.563 1.685 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C3D CLA B 610 " pdb=" CAD CLA B 610 " ideal model delta sigma weight residual 1.454 1.571 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" CAD CLA B 602 " pdb=" CBD CLA B 602 " ideal model delta sigma weight residual 1.563 1.676 -0.113 2.00e-02 2.50e+03 3.22e+01 ... (remaining 20617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 26793 4.08 - 8.16: 1406 8.16 - 12.24: 245 12.24 - 16.32: 42 16.32 - 20.39: 5 Bond angle restraints: 28491 Sorted by residual: angle pdb=" CA GLU C 401 " pdb=" CB GLU C 401 " pdb=" CG GLU C 401 " ideal model delta sigma weight residual 114.10 134.49 -20.39 2.00e+00 2.50e-01 1.04e+02 angle pdb=" N ASP C 348 " pdb=" CA ASP C 348 " pdb=" C ASP C 348 " ideal model delta sigma weight residual 113.17 103.93 9.24 1.26e+00 6.30e-01 5.38e+01 angle pdb=" C1A CLA C 506 " pdb=" C2A CLA C 506 " pdb=" CAA CLA C 506 " ideal model delta sigma weight residual 110.32 90.58 19.74 3.00e+00 1.11e-01 4.33e+01 angle pdb=" CB GLU C 401 " pdb=" CG GLU C 401 " pdb=" CD GLU C 401 " ideal model delta sigma weight residual 112.60 123.61 -11.01 1.70e+00 3.46e-01 4.20e+01 angle pdb=" N SER E 16 " pdb=" CA SER E 16 " pdb=" C SER E 16 " ideal model delta sigma weight residual 108.46 98.84 9.62 1.51e+00 4.39e-01 4.06e+01 ... (remaining 28486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 10060 24.44 - 48.88: 652 48.88 - 73.32: 151 73.32 - 97.76: 63 97.76 - 122.20: 19 Dihedral angle restraints: 10945 sinusoidal: 5048 harmonic: 5897 Sorted by residual: dihedral pdb=" CA MET H 35 " pdb=" C MET H 35 " pdb=" N GLY H 36 " pdb=" CA GLY H 36 " ideal model delta harmonic sigma weight residual 180.00 88.31 91.69 0 5.00e+00 4.00e-02 3.36e+02 dihedral pdb=" CA GLN M 32 " pdb=" C GLN M 32 " pdb=" N GLN M 33 " pdb=" CA GLN M 33 " ideal model delta harmonic sigma weight residual 180.00 -121.37 -58.63 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA ARG y 42 " pdb=" C ARG y 42 " pdb=" N ARG y 43 " pdb=" CA ARG y 43 " ideal model delta harmonic sigma weight residual -180.00 -143.89 -36.11 0 5.00e+00 4.00e-02 5.22e+01 ... (remaining 10942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.807: 2705 0.807 - 1.614: 1 1.614 - 2.420: 0 2.420 - 3.227: 0 3.227 - 4.034: 37 Chirality restraints: 2743 Sorted by residual: chirality pdb=" C8 CLA B 616 " pdb=" C10 CLA B 616 " pdb=" C7 CLA B 616 " pdb=" C9 CLA B 616 " both_signs ideal model delta sigma weight residual False 2.59 -1.44 4.03 2.00e-01 2.50e+01 4.07e+02 chirality pdb=" C8 CLA B 605 " pdb=" C10 CLA B 605 " pdb=" C7 CLA B 605 " pdb=" C9 CLA B 605 " both_signs ideal model delta sigma weight residual False 2.59 -1.33 3.93 2.00e-01 2.50e+01 3.86e+02 chirality pdb=" C8 CLA A 408 " pdb=" C10 CLA A 408 " pdb=" C7 CLA A 408 " pdb=" C9 CLA A 408 " both_signs ideal model delta sigma weight residual False 2.59 -1.25 3.85 2.00e-01 2.50e+01 3.70e+02 ... (remaining 2740 not shown) Planarity restraints: 3565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO A 404 " -0.254 2.00e-02 2.50e+03 2.25e-01 4.04e+03 pdb=" ND PHO A 404 " 0.240 2.00e-02 2.50e+03 pdb=" C1A PHO A 404 " 0.037 2.00e-02 2.50e+03 pdb=" C1B PHO A 404 " -0.135 2.00e-02 2.50e+03 pdb=" C1C PHO A 404 " -0.086 2.00e-02 2.50e+03 pdb=" C1D PHO A 404 " 0.093 2.00e-02 2.50e+03 pdb=" C2A PHO A 404 " -0.209 2.00e-02 2.50e+03 pdb=" C2B PHO A 404 " 0.192 2.00e-02 2.50e+03 pdb=" C2C PHO A 404 " -0.092 2.00e-02 2.50e+03 pdb=" C2D PHO A 404 " 0.045 2.00e-02 2.50e+03 pdb=" C3A PHO A 404 " -0.559 2.00e-02 2.50e+03 pdb=" C3B PHO A 404 " 0.240 2.00e-02 2.50e+03 pdb=" C3C PHO A 404 " -0.056 2.00e-02 2.50e+03 pdb=" C3D PHO A 404 " 0.253 2.00e-02 2.50e+03 pdb=" C4A PHO A 404 " -0.321 2.00e-02 2.50e+03 pdb=" C4B PHO A 404 " -0.048 2.00e-02 2.50e+03 pdb=" C4C PHO A 404 " -0.039 2.00e-02 2.50e+03 pdb=" C4D PHO A 404 " 0.301 2.00e-02 2.50e+03 pdb=" CAB PHO A 404 " 0.385 2.00e-02 2.50e+03 pdb=" CAC PHO A 404 " -0.090 2.00e-02 2.50e+03 pdb=" CAD PHO A 404 " 0.164 2.00e-02 2.50e+03 pdb=" CBD PHO A 404 " 0.296 2.00e-02 2.50e+03 pdb=" CHA PHO A 404 " 0.214 2.00e-02 2.50e+03 pdb=" CHB PHO A 404 " -0.315 2.00e-02 2.50e+03 pdb=" CHC PHO A 404 " -0.084 2.00e-02 2.50e+03 pdb=" CHD PHO A 404 " -0.036 2.00e-02 2.50e+03 pdb=" CMB PHO A 404 " 0.456 2.00e-02 2.50e+03 pdb=" CMC PHO A 404 " -0.140 2.00e-02 2.50e+03 pdb=" CMD PHO A 404 " -0.252 2.00e-02 2.50e+03 pdb=" NA PHO A 404 " -0.097 2.00e-02 2.50e+03 pdb=" NC PHO A 404 " -0.081 2.00e-02 2.50e+03 pdb=" OBD PHO A 404 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 405 " -0.201 2.00e-02 2.50e+03 2.08e-01 3.45e+03 pdb=" ND PHO D 405 " -0.241 2.00e-02 2.50e+03 pdb=" C1A PHO D 405 " 0.014 2.00e-02 2.50e+03 pdb=" C1B PHO D 405 " -0.132 2.00e-02 2.50e+03 pdb=" C1C PHO D 405 " -0.167 2.00e-02 2.50e+03 pdb=" C1D PHO D 405 " -0.199 2.00e-02 2.50e+03 pdb=" C2A PHO D 405 " 0.219 2.00e-02 2.50e+03 pdb=" C2B PHO D 405 " -0.052 2.00e-02 2.50e+03 pdb=" C2C PHO D 405 " 0.129 2.00e-02 2.50e+03 pdb=" C2D PHO D 405 " -0.050 2.00e-02 2.50e+03 pdb=" C3A PHO D 405 " 0.278 2.00e-02 2.50e+03 pdb=" C3B PHO D 405 " -0.014 2.00e-02 2.50e+03 pdb=" C3C PHO D 405 " 0.042 2.00e-02 2.50e+03 pdb=" C3D PHO D 405 " -0.029 2.00e-02 2.50e+03 pdb=" C4A PHO D 405 " 0.075 2.00e-02 2.50e+03 pdb=" C4B PHO D 405 " -0.098 2.00e-02 2.50e+03 pdb=" C4C PHO D 405 " -0.317 2.00e-02 2.50e+03 pdb=" C4D PHO D 405 " -0.138 2.00e-02 2.50e+03 pdb=" CAB PHO D 405 " 0.331 2.00e-02 2.50e+03 pdb=" CAC PHO D 405 " 0.305 2.00e-02 2.50e+03 pdb=" CAD PHO D 405 " 0.155 2.00e-02 2.50e+03 pdb=" CBD PHO D 405 " 0.075 2.00e-02 2.50e+03 pdb=" CHA PHO D 405 " -0.055 2.00e-02 2.50e+03 pdb=" CHB PHO D 405 " -0.040 2.00e-02 2.50e+03 pdb=" CHC PHO D 405 " 0.016 2.00e-02 2.50e+03 pdb=" CHD PHO D 405 " -0.300 2.00e-02 2.50e+03 pdb=" CMB PHO D 405 " -0.080 2.00e-02 2.50e+03 pdb=" CMC PHO D 405 " 0.562 2.00e-02 2.50e+03 pdb=" CMD PHO D 405 " 0.117 2.00e-02 2.50e+03 pdb=" NA PHO D 405 " -0.046 2.00e-02 2.50e+03 pdb=" NC PHO D 405 " -0.422 2.00e-02 2.50e+03 pdb=" OBD PHO D 405 " 0.265 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA C 506 " 0.174 2.00e-02 2.50e+03 1.42e-01 3.04e+02 pdb=" C2A CLA C 506 " -0.224 2.00e-02 2.50e+03 pdb=" C4A CLA C 506 " 0.048 2.00e-02 2.50e+03 pdb=" CHA CLA C 506 " 0.009 2.00e-02 2.50e+03 pdb=" NA CLA C 506 " 0.136 2.00e-02 2.50e+03 pdb="MG CLA C 506 " -0.143 2.00e-02 2.50e+03 ... (remaining 3562 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 41 2.56 - 3.14: 13942 3.14 - 3.73: 29205 3.73 - 4.31: 43998 4.31 - 4.90: 71765 Nonbonded interactions: 158951 Sorted by model distance: nonbonded pdb=" NE2 HIS D 214 " pdb="FE FE A 401 " model vdw 1.974 2.340 nonbonded pdb=" NE2 HIS A 215 " pdb="FE FE A 401 " model vdw 2.069 2.340 nonbonded pdb=" OG1 THR B 128 " pdb=" OE1 GLU B 130 " model vdw 2.213 3.040 nonbonded pdb=" N GLU D 343 " pdb=" OE1 GLU D 343 " model vdw 2.308 3.120 nonbonded pdb=" OE2 GLU C 129 " pdb=" O TYR C 137 " model vdw 2.440 3.040 ... (remaining 158946 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.760 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.022 0.695 20641 Z= 1.749 Angle : 2.158 20.394 28491 Z= 1.024 Chirality : 0.436 4.034 2743 Planarity : 0.018 0.225 3565 Dihedral : 18.805 122.200 7181 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 1.77 % Allowed : 9.81 % Favored : 88.42 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.16), residues: 2056 helix: -1.01 (0.13), residues: 1180 sheet: -0.83 (0.88), residues: 22 loop : -2.28 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.120 0.003 ARG B 384 TYR 0.074 0.011 TYR B 172 PHE 0.074 0.009 PHE I 23 TRP 0.064 0.010 TRP A 131 HIS 0.029 0.004 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.01367 (20622) covalent geometry : angle 2.15758 (28491) hydrogen bonds : bond 0.18168 ( 882) hydrogen bonds : angle 6.52292 ( 2565) Misc. bond : bond 0.55571 ( 19) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 640 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9003 (pt) cc_final: 0.8779 (pt) REVERT: A 136 ARG cc_start: 0.8753 (mmt-90) cc_final: 0.8483 (mmt90) REVERT: A 139 MET cc_start: 0.8843 (ptm) cc_final: 0.8572 (ptm) REVERT: A 191 ASN cc_start: 0.8724 (t0) cc_final: 0.8463 (t0) REVERT: A 319 ASP cc_start: 0.8660 (m-30) cc_final: 0.8446 (m-30) REVERT: B 53 ASN cc_start: 0.8872 (t0) cc_final: 0.8317 (t0) REVERT: B 94 GLU cc_start: 0.8198 (mp0) cc_final: 0.7875 (mp0) REVERT: B 230 ARG cc_start: 0.8215 (mpt180) cc_final: 0.7992 (mmt90) REVERT: B 289 GLN cc_start: 0.9214 (mm110) cc_final: 0.8967 (mm-40) REVERT: B 338 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8540 (mm-40) REVERT: B 423 LYS cc_start: 0.8622 (ptpp) cc_final: 0.8357 (ptpp) REVERT: B 437 LEU cc_start: 0.9051 (mt) cc_final: 0.8767 (mp) REVERT: C 16 GLN cc_start: 0.7822 (pm20) cc_final: 0.7612 (pm20) REVERT: C 55 MET cc_start: 0.8643 (tpt) cc_final: 0.8355 (tpp) REVERT: C 203 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8620 (mtpm) REVERT: C 219 GLU cc_start: 0.8220 (mp0) cc_final: 0.7997 (mp0) REVERT: C 288 GLU cc_start: 0.8279 (mp0) cc_final: 0.7978 (mp0) REVERT: C 354 LEU cc_start: 0.9318 (tt) cc_final: 0.9111 (tm) REVERT: C 355 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7587 (mm-30) REVERT: C 373 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8442 (mm-40) REVERT: C 377 GLU cc_start: 0.8435 (pm20) cc_final: 0.7944 (pm20) REVERT: D 69 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8212 (mt-10) REVERT: D 224 GLN cc_start: 0.8675 (tt0) cc_final: 0.8437 (tt0) REVERT: D 225 ASP cc_start: 0.8431 (m-30) cc_final: 0.8230 (m-30) REVERT: D 233 ARG cc_start: 0.7936 (mtp85) cc_final: 0.6717 (mmt-90) REVERT: D 302 GLU cc_start: 0.8160 (mp0) cc_final: 0.7771 (mp0) REVERT: E 38 VAL cc_start: 0.9533 (t) cc_final: 0.9289 (m) REVERT: E 55 TYR cc_start: 0.9318 (m-80) cc_final: 0.8754 (m-80) REVERT: E 77 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8190 (mt-10) REVERT: H 3 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8020 (ttp-170) REVERT: H 5 THR cc_start: 0.8300 (m) cc_final: 0.7740 (p) REVERT: H 9 ASP cc_start: 0.8741 (m-30) cc_final: 0.7793 (m-30) REVERT: H 20 LYS cc_start: 0.8283 (mptt) cc_final: 0.8036 (mppt) REVERT: H 50 ASN cc_start: 0.9222 (t0) cc_final: 0.9003 (t0) REVERT: I 2 GLU cc_start: 0.8316 (tp30) cc_final: 0.8049 (tp30) REVERT: I 5 LYS cc_start: 0.8461 (tttt) cc_final: 0.8145 (tttm) REVERT: I 31 ASN cc_start: 0.9269 (p0) cc_final: 0.9039 (p0) REVERT: M 29 THR cc_start: 0.8514 (t) cc_final: 0.8123 (t) REVERT: M 30 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7267 (tm-30) REVERT: X 8 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8208 (mtpp) REVERT: y 34 MET cc_start: 0.8287 (tpp) cc_final: 0.7796 (tpp) REVERT: Z 2 THR cc_start: 0.8170 (p) cc_final: 0.7910 (t) REVERT: Z 39 LEU cc_start: 0.9239 (mp) cc_final: 0.8956 (mp) outliers start: 30 outliers final: 12 residues processed: 652 average time/residue: 0.5240 time to fit residues: 391.4629 Evaluate side-chains 478 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 466 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain y residue 24 MET Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 52 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 301 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 274 GLN B 282 GLN B 285 ASN C 366 ASN D 98 GLN ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 164 GLN D 186 GLN D 255 GLN ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN I 31 ASN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN X 33 GLN y 21 GLN Z 31 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.090311 restraints weight = 32510.199| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.60 r_work: 0.2923 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.311 20641 Z= 0.160 Angle : 0.748 12.912 28491 Z= 0.351 Chirality : 0.046 0.274 2743 Planarity : 0.006 0.061 3565 Dihedral : 18.134 122.468 3648 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 4.85 % Allowed : 17.55 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.18), residues: 2056 helix: 0.53 (0.15), residues: 1175 sheet: 0.94 (1.23), residues: 12 loop : -1.51 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 358 TYR 0.020 0.002 TYR K 15 PHE 0.029 0.002 PHE I 23 TRP 0.029 0.002 TRP E 20 HIS 0.007 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00338 (20622) covalent geometry : angle 0.74778 (28491) hydrogen bonds : bond 0.06156 ( 882) hydrogen bonds : angle 4.38438 ( 2565) Misc. bond : bond 0.07204 ( 19) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 492 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8775 (tt0) REVERT: A 333 GLU cc_start: 0.7491 (tp30) cc_final: 0.7015 (tp30) REVERT: B 274 GLN cc_start: 0.9343 (mt0) cc_final: 0.9116 (mt0) REVERT: B 318 ASN cc_start: 0.9267 (t0) cc_final: 0.9062 (t0) REVERT: C 36 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8363 (mptm) REVERT: C 55 MET cc_start: 0.9111 (tpt) cc_final: 0.8799 (tpp) REVERT: C 110 SER cc_start: 0.9031 (t) cc_final: 0.8758 (m) REVERT: C 288 GLU cc_start: 0.8625 (mp0) cc_final: 0.8407 (mp0) REVERT: C 354 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8925 (tm) REVERT: C 373 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8173 (mm110) REVERT: C 377 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8278 (pm20) REVERT: C 409 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8312 (m) REVERT: C 445 LYS cc_start: 0.9070 (mttm) cc_final: 0.8471 (mttm) REVERT: C 448 ASP cc_start: 0.8949 (t0) cc_final: 0.8717 (t0) REVERT: D 69 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8551 (mt-10) REVERT: D 100 ASP cc_start: 0.8895 (t0) cc_final: 0.8572 (t0) REVERT: D 103 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7106 (mmt90) REVERT: D 225 ASP cc_start: 0.8359 (m-30) cc_final: 0.8051 (m-30) REVERT: D 233 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7196 (mpt180) REVERT: D 259 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8983 (pp) REVERT: D 308 ASP cc_start: 0.8150 (t0) cc_final: 0.7808 (t0) REVERT: D 344 GLU cc_start: 0.8948 (pt0) cc_final: 0.8697 (pt0) REVERT: E 55 TYR cc_start: 0.9390 (m-80) cc_final: 0.8873 (m-80) REVERT: E 58 GLN cc_start: 0.8043 (mm110) cc_final: 0.7676 (mm-40) REVERT: H 3 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.8092 (ttm110) REVERT: H 9 ASP cc_start: 0.8409 (m-30) cc_final: 0.7897 (m-30) REVERT: H 20 LYS cc_start: 0.8626 (mptt) cc_final: 0.8358 (mppt) REVERT: H 50 ASN cc_start: 0.9334 (t0) cc_final: 0.8977 (t0) REVERT: H 61 SER cc_start: 0.9355 (t) cc_final: 0.9062 (p) REVERT: I 2 GLU cc_start: 0.8539 (tp30) cc_final: 0.8233 (tp30) REVERT: I 31 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8842 (p0) REVERT: M 30 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7612 (tm-30) REVERT: M 31 SER cc_start: 0.8132 (p) cc_final: 0.7782 (t) REVERT: y 34 MET cc_start: 0.8301 (tpp) cc_final: 0.8071 (tpp) REVERT: Z 2 THR cc_start: 0.8198 (p) cc_final: 0.7854 (t) outliers start: 82 outliers final: 29 residues processed: 521 average time/residue: 0.5213 time to fit residues: 311.2985 Evaluate side-chains 465 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 429 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 51 VAL Chi-restraints excluded: chain Z residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 152 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 115 optimal weight: 0.0970 chunk 148 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN A 252 HIS A 296 ASN A 301 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN D 98 GLN ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.086590 restraints weight = 32930.861| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.59 r_work: 0.2864 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 20641 Z= 0.145 Angle : 0.646 10.431 28491 Z= 0.308 Chirality : 0.044 0.256 2743 Planarity : 0.005 0.057 3565 Dihedral : 16.764 119.745 3632 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Rotamer: Outliers : 4.55 % Allowed : 20.51 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.18), residues: 2056 helix: 1.20 (0.15), residues: 1193 sheet: 1.10 (1.28), residues: 12 loop : -1.14 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 61 TYR 0.015 0.001 TYR A 126 PHE 0.019 0.001 PHE B 246 TRP 0.020 0.001 TRP E 20 HIS 0.006 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00330 (20622) covalent geometry : angle 0.64591 (28491) hydrogen bonds : bond 0.05223 ( 882) hydrogen bonds : angle 4.03055 ( 2565) Misc. bond : bond 0.05633 ( 19) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 452 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7703 (tp30) cc_final: 0.7159 (tp30) REVERT: B 12 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8948 (mp) REVERT: B 37 MET cc_start: 0.9148 (tpt) cc_final: 0.8873 (tpt) REVERT: B 380 ASP cc_start: 0.9188 (p0) cc_final: 0.8717 (p0) REVERT: B 418 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8702 (mtmt) REVERT: C 16 GLN cc_start: 0.7620 (pm20) cc_final: 0.7368 (pm20) REVERT: C 55 MET cc_start: 0.9114 (tpt) cc_final: 0.8858 (tpp) REVERT: C 110 SER cc_start: 0.9145 (t) cc_final: 0.8820 (m) REVERT: C 203 LYS cc_start: 0.9087 (mtpt) cc_final: 0.8642 (mtpm) REVERT: C 209 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8586 (mm-30) REVERT: C 288 GLU cc_start: 0.8723 (mp0) cc_final: 0.8507 (mp0) REVERT: C 296 GLU cc_start: 0.8947 (tt0) cc_final: 0.8710 (tt0) REVERT: C 301 GLN cc_start: 0.8549 (tt0) cc_final: 0.8285 (tt0) REVERT: C 373 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8534 (mm110) REVERT: C 409 SER cc_start: 0.8581 (t) cc_final: 0.8356 (m) REVERT: D 69 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8617 (mt-10) REVERT: D 100 ASP cc_start: 0.8901 (t0) cc_final: 0.8365 (t0) REVERT: D 225 ASP cc_start: 0.8426 (m-30) cc_final: 0.8090 (m-30) REVERT: D 233 ARG cc_start: 0.8224 (mtp85) cc_final: 0.6925 (mmt180) REVERT: D 308 ASP cc_start: 0.8191 (t0) cc_final: 0.7898 (t0) REVERT: E 55 TYR cc_start: 0.9322 (m-80) cc_final: 0.9024 (m-80) REVERT: H 3 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8129 (ttm110) REVERT: H 9 ASP cc_start: 0.8485 (m-30) cc_final: 0.8167 (m-30) REVERT: H 50 ASN cc_start: 0.9223 (t0) cc_final: 0.8933 (t160) REVERT: H 54 ILE cc_start: 0.9432 (mm) cc_final: 0.9208 (mp) REVERT: H 61 SER cc_start: 0.9436 (t) cc_final: 0.9159 (p) REVERT: I 2 GLU cc_start: 0.8512 (tp30) cc_final: 0.8138 (tp30) REVERT: I 31 ASN cc_start: 0.8540 (p0) cc_final: 0.8218 (p0) REVERT: K 18 PHE cc_start: 0.8393 (m-80) cc_final: 0.8142 (m-80) REVERT: L 12 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8778 (tm) REVERT: M 30 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7626 (tm-30) REVERT: M 31 SER cc_start: 0.8041 (p) cc_final: 0.7764 (t) REVERT: X 12 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8426 (mp) REVERT: y 34 MET cc_start: 0.8348 (tpp) cc_final: 0.7958 (tpp) REVERT: Z 2 THR cc_start: 0.8341 (p) cc_final: 0.8022 (t) outliers start: 77 outliers final: 43 residues processed: 481 average time/residue: 0.5304 time to fit residues: 292.3761 Evaluate side-chains 446 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 399 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 33 GLN Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 28 ILE Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 29 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 95 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 chunk 197 optimal weight: 0.0270 chunk 106 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 126 optimal weight: 0.4980 chunk 75 optimal weight: 0.0170 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 191 ASN A 199 GLN A 296 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN B 282 GLN D 106 GLN D 142 ASN D 186 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 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 = 0.3507 r_free = 0.3507 target = 0.118312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.088929 restraints weight = 32589.780| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.58 r_work: 0.2922 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 20641 Z= 0.113 Angle : 0.591 9.772 28491 Z= 0.282 Chirality : 0.041 0.211 2743 Planarity : 0.004 0.055 3565 Dihedral : 15.985 119.780 3630 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 3.61 % Allowed : 23.05 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 2056 helix: 1.44 (0.15), residues: 1205 sheet: 1.06 (1.27), residues: 12 loop : -0.92 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 4 TYR 0.009 0.001 TYR D 315 PHE 0.025 0.001 PHE B 108 TRP 0.018 0.001 TRP E 20 HIS 0.005 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00237 (20622) covalent geometry : angle 0.59133 (28491) hydrogen bonds : bond 0.04237 ( 882) hydrogen bonds : angle 3.84003 ( 2565) Misc. bond : bond 0.05280 ( 19) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 451 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7688 (tp30) cc_final: 0.7053 (tp30) REVERT: B 12 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8956 (mp) REVERT: B 327 THR cc_start: 0.9122 (m) cc_final: 0.8744 (p) REVERT: B 418 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8630 (mtmt) REVERT: C 16 GLN cc_start: 0.7721 (pm20) cc_final: 0.7424 (pm20) REVERT: C 55 MET cc_start: 0.9082 (tpt) cc_final: 0.8842 (tpp) REVERT: C 67 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8222 (ttmm) REVERT: C 85 TRP cc_start: 0.9360 (OUTLIER) cc_final: 0.9100 (m-10) REVERT: C 110 SER cc_start: 0.9196 (t) cc_final: 0.8867 (m) REVERT: C 203 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8606 (mtpm) REVERT: C 209 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8441 (mm-30) REVERT: C 288 GLU cc_start: 0.8724 (mp0) cc_final: 0.8503 (mp0) REVERT: C 296 GLU cc_start: 0.8971 (tt0) cc_final: 0.8725 (tt0) REVERT: C 301 GLN cc_start: 0.8477 (tt0) cc_final: 0.8255 (tt0) REVERT: C 303 MET cc_start: 0.9117 (tpp) cc_final: 0.8645 (tmm) REVERT: C 409 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.7963 (p) REVERT: D 25 ASP cc_start: 0.8625 (p0) cc_final: 0.8227 (t70) REVERT: D 69 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8619 (mt-10) REVERT: D 100 ASP cc_start: 0.8980 (t0) cc_final: 0.8364 (t0) REVERT: D 225 ASP cc_start: 0.8452 (m-30) cc_final: 0.8085 (m-30) REVERT: D 233 ARG cc_start: 0.8246 (mtp85) cc_final: 0.6982 (mmt180) REVERT: D 344 GLU cc_start: 0.8833 (pt0) cc_final: 0.8614 (pt0) REVERT: H 3 ARG cc_start: 0.8394 (ttm-80) cc_final: 0.8175 (ttm110) REVERT: H 9 ASP cc_start: 0.8373 (m-30) cc_final: 0.8167 (m-30) REVERT: H 50 ASN cc_start: 0.9147 (t0) cc_final: 0.8782 (t160) REVERT: H 61 SER cc_start: 0.9393 (t) cc_final: 0.9154 (p) REVERT: I 31 ASN cc_start: 0.8693 (p0) cc_final: 0.8364 (p0) REVERT: M 30 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7424 (tm-30) REVERT: T 1 MET cc_start: 0.6917 (tpp) cc_final: 0.6510 (ttt) REVERT: T 24 ARG cc_start: 0.8941 (ptt180) cc_final: 0.8733 (ptt-90) REVERT: X 8 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8314 (mtpp) REVERT: y 34 MET cc_start: 0.8365 (tpp) cc_final: 0.8009 (tpp) REVERT: Z 2 THR cc_start: 0.8332 (p) cc_final: 0.8009 (t) outliers start: 61 outliers final: 30 residues processed: 474 average time/residue: 0.4902 time to fit residues: 269.3874 Evaluate side-chains 447 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 413 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 28 ILE Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 29 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 181 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 296 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN D 129 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.082550 restraints weight = 32707.017| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.57 r_work: 0.2770 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 20641 Z= 0.169 Angle : 0.635 10.487 28491 Z= 0.303 Chirality : 0.044 0.254 2743 Planarity : 0.005 0.057 3565 Dihedral : 15.557 119.155 3628 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 4.43 % Allowed : 22.64 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 2056 helix: 1.59 (0.15), residues: 1202 sheet: 1.29 (1.28), residues: 12 loop : -0.77 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Z 35 TYR 0.018 0.001 TYR A 246 PHE 0.021 0.002 PHE A 273 TRP 0.020 0.001 TRP F 20 HIS 0.007 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00381 (20622) covalent geometry : angle 0.63482 (28491) hydrogen bonds : bond 0.05357 ( 882) hydrogen bonds : angle 3.90364 ( 2565) Misc. bond : bond 0.05891 ( 19) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 421 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 296 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8037 (t0) REVERT: A 333 GLU cc_start: 0.7659 (tp30) cc_final: 0.7065 (tp30) REVERT: B 44 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8717 (t) REVERT: B 318 ASN cc_start: 0.9261 (t0) cc_final: 0.8905 (t0) REVERT: B 327 THR cc_start: 0.9270 (m) cc_final: 0.9069 (p) REVERT: B 418 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8696 (mtmt) REVERT: B 476 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8446 (ttp80) REVERT: C 16 GLN cc_start: 0.7507 (pm20) cc_final: 0.7212 (pm20) REVERT: C 67 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8463 (ttmm) REVERT: C 85 TRP cc_start: 0.9389 (OUTLIER) cc_final: 0.9137 (m-10) REVERT: C 203 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8721 (mtpm) REVERT: C 296 GLU cc_start: 0.9029 (tt0) cc_final: 0.8766 (tt0) REVERT: C 409 SER cc_start: 0.8659 (t) cc_final: 0.8169 (p) REVERT: D 25 ASP cc_start: 0.8670 (p0) cc_final: 0.8350 (t70) REVERT: D 100 ASP cc_start: 0.9048 (t0) cc_final: 0.8392 (t0) REVERT: D 225 ASP cc_start: 0.8588 (m-30) cc_final: 0.8368 (m-30) REVERT: D 233 ARG cc_start: 0.8316 (mtp85) cc_final: 0.7092 (mmt180) REVERT: E 62 SER cc_start: 0.9185 (t) cc_final: 0.8848 (p) REVERT: H 3 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8159 (ttm110) REVERT: H 50 ASN cc_start: 0.9085 (t0) cc_final: 0.8734 (t160) REVERT: H 61 SER cc_start: 0.9504 (t) cc_final: 0.9187 (p) REVERT: I 31 ASN cc_start: 0.8639 (p0) cc_final: 0.8363 (p0) REVERT: L 12 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8789 (tm) REVERT: M 30 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7360 (tm-30) REVERT: M 31 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7507 (t) REVERT: T 24 ARG cc_start: 0.9112 (ptt180) cc_final: 0.8879 (ptt-90) REVERT: X 8 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8059 (mtpp) REVERT: X 12 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8610 (mp) REVERT: y 34 MET cc_start: 0.8430 (tpp) cc_final: 0.8105 (tpp) REVERT: Z 2 THR cc_start: 0.8329 (p) cc_final: 0.8021 (t) outliers start: 75 outliers final: 41 residues processed: 454 average time/residue: 0.4821 time to fit residues: 253.5523 Evaluate side-chains 434 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 385 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 28 ILE Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 25 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 140 optimal weight: 0.0270 chunk 114 optimal weight: 0.7980 chunk 200 optimal weight: 0.0170 chunk 136 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 187 GLN A 247 ASN A 252 HIS A 301 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 220 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.086123 restraints weight = 32490.756| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.57 r_work: 0.2861 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.162 20641 Z= 0.118 Angle : 0.602 10.205 28491 Z= 0.288 Chirality : 0.042 0.223 2743 Planarity : 0.004 0.055 3565 Dihedral : 15.063 119.513 3628 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 2.78 % Allowed : 25.24 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.19), residues: 2056 helix: 1.71 (0.15), residues: 1198 sheet: 1.36 (1.29), residues: 12 loop : -0.65 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 422 TYR 0.013 0.001 TYR K 15 PHE 0.028 0.001 PHE B 108 TRP 0.017 0.001 TRP F 20 HIS 0.006 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00256 (20622) covalent geometry : angle 0.60230 (28491) hydrogen bonds : bond 0.04324 ( 882) hydrogen bonds : angle 3.74817 ( 2565) Misc. bond : bond 0.05199 ( 19) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 420 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7712 (tm-30) cc_final: 0.6565 (tm-30) REVERT: B 44 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8719 (t) REVERT: B 179 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8437 (mm-40) REVERT: B 476 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8312 (ttp80) REVERT: C 16 GLN cc_start: 0.7559 (pm20) cc_final: 0.7242 (pm20) REVERT: C 55 MET cc_start: 0.9114 (tpt) cc_final: 0.8817 (tpt) REVERT: C 85 TRP cc_start: 0.9386 (OUTLIER) cc_final: 0.9149 (m-10) REVERT: C 303 MET cc_start: 0.9182 (tmm) cc_final: 0.8791 (tmm) REVERT: C 409 SER cc_start: 0.8509 (t) cc_final: 0.8134 (p) REVERT: D 16 ASP cc_start: 0.7648 (p0) cc_final: 0.7135 (p0) REVERT: D 20 ASP cc_start: 0.8901 (p0) cc_final: 0.8333 (p0) REVERT: D 25 ASP cc_start: 0.8649 (p0) cc_final: 0.8381 (t70) REVERT: D 100 ASP cc_start: 0.9047 (t0) cc_final: 0.8381 (t0) REVERT: D 225 ASP cc_start: 0.8552 (m-30) cc_final: 0.8283 (m-30) REVERT: D 233 ARG cc_start: 0.8305 (mtp85) cc_final: 0.7105 (mmt180) REVERT: E 55 TYR cc_start: 0.9124 (m-80) cc_final: 0.8862 (m-80) REVERT: E 62 SER cc_start: 0.9259 (t) cc_final: 0.8923 (p) REVERT: H 4 ARG cc_start: 0.9150 (mmm-85) cc_final: 0.8904 (mmm-85) REVERT: H 9 ASP cc_start: 0.8679 (m-30) cc_final: 0.8132 (m-30) REVERT: H 50 ASN cc_start: 0.9028 (t0) cc_final: 0.8569 (t160) REVERT: H 61 SER cc_start: 0.9470 (OUTLIER) cc_final: 0.9189 (p) REVERT: I 31 ASN cc_start: 0.8581 (p0) cc_final: 0.8300 (p0) REVERT: L 12 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8787 (tm) REVERT: X 8 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8350 (mtpp) REVERT: y 34 MET cc_start: 0.8440 (tpp) cc_final: 0.8205 (tpp) REVERT: Z 2 THR cc_start: 0.8425 (p) cc_final: 0.8118 (t) outliers start: 47 outliers final: 33 residues processed: 441 average time/residue: 0.4806 time to fit residues: 246.1382 Evaluate side-chains 438 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 400 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 28 ILE Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 29 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 198 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 159 optimal weight: 0.0030 chunk 57 optimal weight: 0.9980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 252 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 186 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.084732 restraints weight = 32680.767| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.57 r_work: 0.2825 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 20641 Z= 0.124 Angle : 0.611 12.110 28491 Z= 0.293 Chirality : 0.042 0.223 2743 Planarity : 0.004 0.054 3565 Dihedral : 14.682 119.239 3627 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 3.25 % Allowed : 25.59 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 2056 helix: 1.76 (0.15), residues: 1199 sheet: 1.52 (1.34), residues: 12 loop : -0.53 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 422 TYR 0.017 0.001 TYR A 246 PHE 0.020 0.001 PHE A 260 TRP 0.019 0.001 TRP F 20 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00279 (20622) covalent geometry : angle 0.61086 (28491) hydrogen bonds : bond 0.04342 ( 882) hydrogen bonds : angle 3.73671 ( 2565) Misc. bond : bond 0.04829 ( 19) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 415 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7674 (mp0) cc_final: 0.7386 (tt0) REVERT: B 12 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9193 (mp) REVERT: B 44 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8777 (t) REVERT: B 179 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8376 (mm-40) REVERT: B 476 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8326 (ttp80) REVERT: C 16 GLN cc_start: 0.7571 (pm20) cc_final: 0.7250 (pm20) REVERT: C 55 MET cc_start: 0.9109 (tpt) cc_final: 0.8742 (tpt) REVERT: C 85 TRP cc_start: 0.9381 (OUTLIER) cc_final: 0.9134 (m-10) REVERT: C 203 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8728 (mtpm) REVERT: C 303 MET cc_start: 0.9149 (tmm) cc_final: 0.8799 (tmm) REVERT: C 369 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8751 (mtmm) REVERT: C 409 SER cc_start: 0.8516 (t) cc_final: 0.8149 (p) REVERT: D 25 ASP cc_start: 0.8616 (p0) cc_final: 0.8337 (t70) REVERT: D 100 ASP cc_start: 0.9081 (t0) cc_final: 0.8410 (t0) REVERT: D 225 ASP cc_start: 0.8605 (m-30) cc_final: 0.8404 (m-30) REVERT: D 233 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7123 (mmt180) REVERT: E 62 SER cc_start: 0.9271 (t) cc_final: 0.8947 (p) REVERT: H 9 ASP cc_start: 0.8707 (m-30) cc_final: 0.8299 (m-30) REVERT: H 50 ASN cc_start: 0.9072 (t0) cc_final: 0.8623 (t160) REVERT: H 61 SER cc_start: 0.9484 (t) cc_final: 0.9195 (p) REVERT: I 31 ASN cc_start: 0.8481 (p0) cc_final: 0.8237 (p0) REVERT: L 12 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8762 (tm) REVERT: T 1 MET cc_start: 0.7290 (tpp) cc_final: 0.6524 (ttp) REVERT: X 8 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8003 (mtpp) REVERT: X 12 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8530 (mp) REVERT: y 34 MET cc_start: 0.8441 (tpp) cc_final: 0.8207 (tpp) outliers start: 55 outliers final: 41 residues processed: 438 average time/residue: 0.4935 time to fit residues: 250.4629 Evaluate side-chains 439 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 392 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 28 ILE Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 58 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 72 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 107 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 252 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS D 129 GLN Z 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.081142 restraints weight = 32726.432| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.54 r_work: 0.2773 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.187 20641 Z= 0.184 Angle : 0.661 12.434 28491 Z= 0.317 Chirality : 0.045 0.243 2743 Planarity : 0.005 0.059 3565 Dihedral : 14.620 119.797 3627 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 3.72 % Allowed : 26.36 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 2056 helix: 1.72 (0.15), residues: 1200 sheet: 1.67 (1.35), residues: 12 loop : -0.48 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 422 TYR 0.015 0.001 TYR B 273 PHE 0.034 0.001 PHE B 108 TRP 0.024 0.001 TRP F 20 HIS 0.007 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00424 (20622) covalent geometry : angle 0.66112 (28491) hydrogen bonds : bond 0.05277 ( 882) hydrogen bonds : angle 3.85788 ( 2565) Misc. bond : bond 0.05525 ( 19) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 404 time to evaluate : 0.693 Fit side-chains REVERT: A 243 GLU cc_start: 0.7677 (mp0) cc_final: 0.7454 (tt0) REVERT: B 476 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8514 (ttp80) REVERT: C 16 GLN cc_start: 0.7615 (pm20) cc_final: 0.7324 (pm20) REVERT: C 85 TRP cc_start: 0.9420 (OUTLIER) cc_final: 0.9171 (m-10) REVERT: C 303 MET cc_start: 0.9150 (tmm) cc_final: 0.8889 (tmm) REVERT: C 409 SER cc_start: 0.8600 (t) cc_final: 0.8190 (p) REVERT: D 25 ASP cc_start: 0.8588 (p0) cc_final: 0.8324 (t70) REVERT: D 27 PHE cc_start: 0.8497 (t80) cc_final: 0.8197 (t80) REVERT: D 96 GLU cc_start: 0.8303 (mp0) cc_final: 0.8098 (mp0) REVERT: D 100 ASP cc_start: 0.9054 (t0) cc_final: 0.8399 (t0) REVERT: D 225 ASP cc_start: 0.8659 (m-30) cc_final: 0.8404 (m-30) REVERT: D 233 ARG cc_start: 0.8356 (mtp85) cc_final: 0.7135 (mmt180) REVERT: D 295 SER cc_start: 0.9343 (t) cc_final: 0.9043 (p) REVERT: D 302 GLU cc_start: 0.8406 (mp0) cc_final: 0.8129 (mp0) REVERT: E 62 SER cc_start: 0.9266 (t) cc_final: 0.8922 (p) REVERT: H 4 ARG cc_start: 0.9230 (mmm-85) cc_final: 0.8970 (mmm-85) REVERT: H 9 ASP cc_start: 0.8744 (m-30) cc_final: 0.8428 (m-30) REVERT: H 50 ASN cc_start: 0.9141 (t0) cc_final: 0.8719 (t160) REVERT: H 61 SER cc_start: 0.9555 (OUTLIER) cc_final: 0.9252 (p) REVERT: I 31 ASN cc_start: 0.8485 (p0) cc_final: 0.8226 (p0) REVERT: L 1 MET cc_start: -0.2195 (OUTLIER) cc_final: -0.2994 (mtt) REVERT: L 11 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8030 (tm-30) REVERT: L 12 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8850 (tm) REVERT: T 1 MET cc_start: 0.7332 (tpp) cc_final: 0.6689 (ttp) REVERT: X 8 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8115 (mtpp) REVERT: X 12 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8732 (mp) REVERT: y 34 MET cc_start: 0.8492 (tpp) cc_final: 0.8236 (tpp) outliers start: 63 outliers final: 42 residues processed: 432 average time/residue: 0.4894 time to fit residues: 245.9951 Evaluate side-chains 430 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 382 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 28 ILE Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 25 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS D 129 GLN D 220 ASN Z 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.082154 restraints weight = 32436.563| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.55 r_work: 0.2787 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 20641 Z= 0.154 Angle : 0.660 11.794 28491 Z= 0.316 Chirality : 0.044 0.243 2743 Planarity : 0.005 0.063 3565 Dihedral : 14.484 119.859 3627 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 3.37 % Allowed : 26.48 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.19), residues: 2056 helix: 1.75 (0.15), residues: 1199 sheet: 1.72 (1.38), residues: 12 loop : -0.44 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 422 TYR 0.018 0.001 TYR A 246 PHE 0.022 0.001 PHE A 260 TRP 0.021 0.001 TRP F 20 HIS 0.004 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00357 (20622) covalent geometry : angle 0.65972 (28491) hydrogen bonds : bond 0.04950 ( 882) hydrogen bonds : angle 3.84571 ( 2565) Misc. bond : bond 0.05285 ( 19) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 401 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7799 (mp0) cc_final: 0.7568 (tt0) REVERT: B 418 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8724 (mtmt) REVERT: B 422 ARG cc_start: 0.9083 (ptp-110) cc_final: 0.8809 (ttp80) REVERT: B 476 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8460 (ttp80) REVERT: C 16 GLN cc_start: 0.7587 (pm20) cc_final: 0.7297 (pm20) REVERT: C 85 TRP cc_start: 0.9416 (OUTLIER) cc_final: 0.9132 (m-10) REVERT: C 303 MET cc_start: 0.9147 (tmm) cc_final: 0.8866 (tmm) REVERT: C 384 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8653 (mtp) REVERT: C 409 SER cc_start: 0.8562 (t) cc_final: 0.8147 (p) REVERT: D 25 ASP cc_start: 0.8577 (p0) cc_final: 0.8315 (t70) REVERT: D 69 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8504 (mt-10) REVERT: D 100 ASP cc_start: 0.9037 (t0) cc_final: 0.8369 (t0) REVERT: D 225 ASP cc_start: 0.8657 (m-30) cc_final: 0.8400 (m-30) REVERT: D 233 ARG cc_start: 0.8361 (mtp85) cc_final: 0.7221 (mmt180) REVERT: D 295 SER cc_start: 0.9325 (t) cc_final: 0.9029 (p) REVERT: D 302 GLU cc_start: 0.8272 (mp0) cc_final: 0.7915 (mp0) REVERT: E 62 SER cc_start: 0.9261 (t) cc_final: 0.8906 (p) REVERT: H 4 ARG cc_start: 0.9214 (mmm-85) cc_final: 0.8937 (mmm-85) REVERT: H 9 ASP cc_start: 0.8732 (m-30) cc_final: 0.8133 (m-30) REVERT: H 35 MET cc_start: 0.8965 (ttm) cc_final: 0.8740 (mtp) REVERT: H 50 ASN cc_start: 0.9089 (t0) cc_final: 0.8645 (t160) REVERT: H 61 SER cc_start: 0.9549 (OUTLIER) cc_final: 0.9237 (p) REVERT: I 31 ASN cc_start: 0.8457 (p0) cc_final: 0.8214 (p0) REVERT: L 1 MET cc_start: -0.2011 (OUTLIER) cc_final: -0.2824 (mtt) REVERT: L 11 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8022 (tm-30) REVERT: L 12 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8876 (tm) REVERT: T 1 MET cc_start: 0.7296 (tpp) cc_final: 0.6664 (ttp) REVERT: X 8 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8396 (mtpp) REVERT: y 34 MET cc_start: 0.8491 (tpp) cc_final: 0.8232 (tpp) REVERT: Z 2 THR cc_start: 0.8444 (p) cc_final: 0.8138 (t) outliers start: 57 outliers final: 41 residues processed: 428 average time/residue: 0.4741 time to fit residues: 235.6270 Evaluate side-chains 439 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 391 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 28 ILE Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 51 VAL Chi-restraints excluded: chain Z residue 58 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 199 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 163 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 117 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 296 ASN A 301 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 332 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.083895 restraints weight = 32602.085| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.52 r_work: 0.2836 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.158 20641 Z= 0.128 Angle : 0.641 11.718 28491 Z= 0.309 Chirality : 0.043 0.229 2743 Planarity : 0.004 0.060 3565 Dihedral : 14.308 119.718 3627 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 2.60 % Allowed : 27.72 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 2056 helix: 1.75 (0.15), residues: 1201 sheet: 1.78 (1.42), residues: 12 loop : -0.35 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 422 TYR 0.010 0.001 TYR M 26 PHE 0.030 0.001 PHE B 108 TRP 0.020 0.001 TRP F 20 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00290 (20622) covalent geometry : angle 0.64139 (28491) hydrogen bonds : bond 0.04455 ( 882) hydrogen bonds : angle 3.78500 ( 2565) Misc. bond : bond 0.04777 ( 19) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 402 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 296 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.8063 (t0) REVERT: B 418 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8653 (mtmt) REVERT: B 476 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8378 (ttp80) REVERT: C 16 GLN cc_start: 0.7655 (pm20) cc_final: 0.7328 (pm20) REVERT: C 85 TRP cc_start: 0.9422 (OUTLIER) cc_final: 0.9127 (m-10) REVERT: C 303 MET cc_start: 0.9141 (tmm) cc_final: 0.8770 (tmm) REVERT: C 384 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8612 (mtp) REVERT: C 409 SER cc_start: 0.8528 (t) cc_final: 0.8131 (p) REVERT: D 25 ASP cc_start: 0.8562 (p0) cc_final: 0.8304 (t70) REVERT: D 100 ASP cc_start: 0.9066 (t0) cc_final: 0.8396 (t0) REVERT: D 225 ASP cc_start: 0.8678 (m-30) cc_final: 0.8417 (m-30) REVERT: D 233 ARG cc_start: 0.8354 (mtp85) cc_final: 0.7210 (mmt180) REVERT: D 295 SER cc_start: 0.9304 (t) cc_final: 0.8968 (p) REVERT: D 302 GLU cc_start: 0.8329 (mp0) cc_final: 0.7996 (mp0) REVERT: E 62 SER cc_start: 0.9254 (t) cc_final: 0.8879 (p) REVERT: H 4 ARG cc_start: 0.9205 (mmm-85) cc_final: 0.8935 (mmm-85) REVERT: H 9 ASP cc_start: 0.8726 (m-30) cc_final: 0.8092 (m-30) REVERT: H 50 ASN cc_start: 0.9088 (t0) cc_final: 0.8632 (t160) REVERT: H 61 SER cc_start: 0.9526 (OUTLIER) cc_final: 0.9226 (p) REVERT: I 31 ASN cc_start: 0.8404 (p0) cc_final: 0.8164 (p0) REVERT: L 1 MET cc_start: -0.1979 (OUTLIER) cc_final: -0.2586 (mtt) REVERT: L 11 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7967 (tm-30) REVERT: L 12 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8875 (tm) REVERT: T 1 MET cc_start: 0.7305 (tpp) cc_final: 0.6599 (ttm) REVERT: X 8 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8406 (mtpp) REVERT: y 27 MET cc_start: 0.8280 (ppp) cc_final: 0.6989 (pmt) REVERT: y 34 MET cc_start: 0.8488 (tpp) cc_final: 0.8237 (tpp) REVERT: Z 2 THR cc_start: 0.8450 (p) cc_final: 0.8107 (t) outliers start: 44 outliers final: 28 residues processed: 420 average time/residue: 0.4836 time to fit residues: 235.0019 Evaluate side-chains 430 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 394 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 28 ILE Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 157 optimal weight: 0.7980 chunk 130 optimal weight: 0.0050 chunk 183 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 181 optimal weight: 0.0010 chunk 152 optimal weight: 3.9990 chunk 195 optimal weight: 0.1980 chunk 146 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 129 GLN D 332 GLN D 336 HIS ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.085501 restraints weight = 32630.098| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.54 r_work: 0.2845 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 20641 Z= 0.120 Angle : 0.636 11.491 28491 Z= 0.303 Chirality : 0.042 0.207 2743 Planarity : 0.005 0.071 3565 Dihedral : 14.112 119.432 3627 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.42 % Rotamer: Outliers : 2.30 % Allowed : 28.19 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 2056 helix: 1.78 (0.15), residues: 1201 sheet: 1.74 (1.45), residues: 12 loop : -0.28 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG Z 35 TYR 0.022 0.001 TYR A 246 PHE 0.021 0.001 PHE A 260 TRP 0.020 0.001 TRP F 20 HIS 0.002 0.001 HIS F 24 Details of bonding type rmsd covalent geometry : bond 0.00267 (20622) covalent geometry : angle 0.63580 (28491) hydrogen bonds : bond 0.04061 ( 882) hydrogen bonds : angle 3.74194 ( 2565) Misc. bond : bond 0.04274 ( 19) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6865.83 seconds wall clock time: 117 minutes 16.12 seconds (7036.12 seconds total)