Starting phenix.real_space_refine on Thu Sep 18 20:58:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zee_60026/09_2025/8zee_60026_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zee_60026/09_2025/8zee_60026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zee_60026/09_2025/8zee_60026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zee_60026/09_2025/8zee_60026.map" model { file = "/net/cci-nas-00/data/ceres_data/8zee_60026/09_2025/8zee_60026_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zee_60026/09_2025/8zee_60026_neut.cif" } resolution = 2.9 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= 0.005 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 8 5.49 5 Mg 35 5.21 5 S 66 5.16 5 C 14044 2.51 5 N 2838 2.21 5 O 3225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20218 Number of models: 1 Model: "" Number of chains: 26 Chain: "B" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3766 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 25, 'TRANS': 456} Chain: "D" Number of atoms: 2791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2791 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain: "E" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "F" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 277 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "H" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 561 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain: "I" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "K" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "L" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 314 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "M" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 239 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "T" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "V" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 224 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "X" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 242 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "Z" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 458 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "C" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3368 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 24, 'TRANS': 405} Chain breaks: 2 Chain: "A" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2418 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain breaks: 1 Chain: "1" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 313 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "B" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 1326 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 3, 'LMG': 1} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 609 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 3, 'LMG': 1, 'PHO': 2, 'PL9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 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: "H" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCR': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "K" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'BCR': 1, 'LHG': 1, 'LMG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'VTQ': 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} Chain: "C" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1244 Unusual residues: {'BCR': 2, 'CLA': 13, 'DGD': 3, 'LMG': 2, 'SQD': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'BCR': 1, 'CLA': 3, 'FE2': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.85, per 1000 atoms: 0.24 Number of scatterers: 20218 At special positions: 0 Unit cell: (113.4, 136.35, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 66 16.00 P 8 15.00 Mg 35 11.99 O 3225 8.00 N 2838 7.00 C 14044 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=29, symmetry=0 Number of additional bonds: simple=29, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 581.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3786 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 8 sheets defined 67.4% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 4 through 13 removed outlier: 4.035A pdb=" N VAL B 8 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N HIS B 9 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 10 " --> pdb=" O ARG B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 45 removed outlier: 3.582A pdb=" N LEU B 19 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.904A pdb=" N LEU B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.568A pdb=" N PHE B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 219 removed outlier: 3.945A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY B 206 " --> pdb=" O HIS B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 235 through 259 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.812A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 295 Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.626A pdb=" N TRP B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 30 through 54 removed outlier: 4.131A pdb=" N LEU D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 108 through 137 removed outlier: 4.332A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 164 Proline residue: D 149 - end of helix removed outlier: 4.248A pdb=" N TYR D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 175 through 189 Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 194 through 220 Processing helix chain 'D' and resid 245 through 257 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 275 - end of helix removed outlier: 4.060A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 334 removed outlier: 4.439A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN D 332 " --> pdb=" O TRP D 328 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'E' and resid 9 through 15 removed outlier: 3.723A pdb=" N ILE E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 40 removed outlier: 4.192A pdb=" N TRP E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 41 through 48 removed outlier: 3.669A pdb=" N ASP E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 55 removed outlier: 4.102A pdb=" N TYR E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 81 Processing helix chain 'F' and resid 16 through 41 removed outlier: 3.693A pdb=" N ILE F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Proline residue: F 28 - end of helix removed outlier: 3.998A pdb=" N PHE F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 31 Processing helix chain 'H' and resid 32 through 35 removed outlier: 3.630A pdb=" N SER H 35 " --> pdb=" O PRO H 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 32 through 35' Processing helix chain 'H' and resid 46 through 69 removed outlier: 3.652A pdb=" N MET H 50 " --> pdb=" O THR H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 85 Processing helix chain 'I' and resid 2 through 24 Processing helix chain 'K' and resid 12 through 17 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 18 through 23 removed outlier: 3.742A pdb=" N VAL K 22 " --> pdb=" O PHE K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 27 Processing helix chain 'K' and resid 28 through 42 removed outlier: 3.545A pdb=" N PHE K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 38 removed outlier: 4.713A pdb=" N SER L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 31 Proline residue: M 18 - end of helix removed outlier: 3.601A pdb=" N SER M 31 " --> pdb=" O VAL M 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'V' and resid 3 through 18 Processing helix chain 'V' and resid 19 through 29 removed outlier: 3.892A pdb=" N VAL V 23 " --> pdb=" O GLY V 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 98 Processing helix chain 'Z' and resid 2 through 29 Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 36 through 60 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 22 through 31 removed outlier: 5.885A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 62 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.189A pdb=" N GLY C 73 " --> pdb=" O TYR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'C' and resid 96 through 123 removed outlier: 3.884A pdb=" N PHE C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 170 Processing helix chain 'C' and resid 193 through 200 removed outlier: 4.004A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.549A pdb=" N ILE C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 281 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 293 through 313 Processing helix chain 'C' and resid 340 through 347 removed outlier: 4.309A pdb=" N THR C 343 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG C 345 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP C 347 " --> pdb=" O MET C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 373 through 385 removed outlier: 4.042A pdb=" N THR C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 442 removed outlier: 3.515A 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 'A' and resid 12 through 23 Processing helix chain 'A' and resid 30 through 55 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 109 through 138 removed outlier: 4.108A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP A 131 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 166 removed outlier: 4.208A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix removed outlier: 4.742A pdb=" N TYR A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.510A pdb=" N ASP A 170 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 191 through 194 removed outlier: 3.558A pdb=" N MET A 194 " --> pdb=" O ASN A 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 194' Processing helix chain 'A' and resid 195 through 223 Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.764A pdb=" N TYR A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 295 removed outlier: 3.626A pdb=" N HIS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.573A pdb=" N PHE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.584A pdb=" N GLY A 311 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A 312 " --> pdb=" O SER A 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 312' Processing helix chain 'A' and resid 316 through 333 Processing helix chain '1' and resid 44 through 57 removed outlier: 3.665A pdb=" N ALA 1 48 " --> pdb=" O PRO 1 44 " (cutoff:3.500A) Processing helix chain '1' and resid 62 through 78 removed outlier: 3.729A pdb=" N LEU 1 67 " --> pdb=" O ILE 1 63 " (cutoff:3.500A) Proline residue: 1 69 - end of helix removed outlier: 3.677A pdb=" N ASP 1 75 " --> pdb=" O GLN 1 71 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS 1 76 " --> pdb=" O GLN 1 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 166 through 169 Processing sheet with id=AA2, first strand: chain 'B' and resid 322 through 323 removed outlier: 6.953A pdb=" N GLY B 322 " --> pdb=" O ARG D 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.748A pdb=" N GLU B 431 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 6.822A pdb=" N LEU B 370 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 77 through 78 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 330 through 331 Processing sheet with id=AA8, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.507A pdb=" N LEU A 174 " --> pdb=" O VAL A 82 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 5805 1.37 - 1.55: 14901 1.55 - 1.73: 69 1.73 - 1.92: 113 1.92 - 2.10: 144 Bond restraints: 21032 Sorted by residual: bond pdb=" C6 SQD C 620 " pdb=" S SQD C 620 " ideal model delta sigma weight residual 1.840 1.662 0.178 2.00e-02 2.50e+03 7.95e+01 bond pdb=" C7 LHG B 622 " pdb=" O7 LHG B 622 " ideal model delta sigma weight residual 1.329 1.457 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C7 LHG B 621 " pdb=" O7 LHG B 621 " ideal model delta sigma weight residual 1.329 1.457 -0.128 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C7 LHG D 407 " pdb=" O7 LHG D 407 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C7 LHG K 103 " pdb=" O7 LHG K 103 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.02e+01 ... (remaining 21027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 28476 3.69 - 7.38: 403 7.38 - 11.07: 52 11.07 - 14.76: 33 14.76 - 18.45: 33 Bond angle restraints: 28997 Sorted by residual: angle pdb=" NB CLA B 609 " pdb="MG CLA B 609 " pdb=" ND CLA B 609 " ideal model delta sigma weight residual 176.90 158.45 18.45 3.00e+00 1.11e-01 3.78e+01 angle pdb=" NB CLA C 604 " pdb="MG CLA C 604 " pdb=" ND CLA C 604 " ideal model delta sigma weight residual 176.90 158.74 18.16 3.00e+00 1.11e-01 3.66e+01 angle pdb=" NB CLA C 613 " pdb="MG CLA C 613 " pdb=" ND CLA C 613 " ideal model delta sigma weight residual 176.90 159.00 17.90 3.00e+00 1.11e-01 3.56e+01 angle pdb=" NB CLA C 606 " pdb="MG CLA C 606 " pdb=" ND CLA C 606 " ideal model delta sigma weight residual 176.90 159.24 17.66 3.00e+00 1.11e-01 3.47e+01 angle pdb=" NB CLA B 604 " pdb="MG CLA B 604 " pdb=" ND CLA B 604 " ideal model delta sigma weight residual 176.90 159.27 17.63 3.00e+00 1.11e-01 3.45e+01 ... (remaining 28992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 10524 27.04 - 54.09: 696 54.09 - 81.13: 89 81.13 - 108.17: 22 108.17 - 135.21: 22 Dihedral angle restraints: 11353 sinusoidal: 5421 harmonic: 5932 Sorted by residual: dihedral pdb=" CA LEU A 297 " pdb=" C LEU A 297 " pdb=" N ASN A 298 " pdb=" CA ASN A 298 " ideal model delta harmonic sigma weight residual 180.00 152.88 27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" C3A DGD C 617 " pdb=" C1A DGD C 617 " pdb=" C2A DGD C 617 " pdb=" O1A DGD C 617 " ideal model delta sinusoidal sigma weight residual -24.22 110.99 -135.21 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C4D PHO D 412 " pdb=" CBD PHO D 412 " pdb=" CHA PHO D 412 " pdb=" CGD PHO D 412 " ideal model delta sinusoidal sigma weight residual 243.52 115.25 128.27 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 11350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2200 0.044 - 0.088: 468 0.088 - 0.132: 124 0.132 - 0.177: 8 0.177 - 0.221: 9 Chirality restraints: 2809 Sorted by residual: chirality pdb=" C18 VTQ X 201 " pdb=" C17 VTQ X 201 " pdb=" C19 VTQ X 201 " pdb=" C20 VTQ X 201 " both_signs ideal model delta sigma weight residual False 2.57 2.79 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C2 LHG D 407 " pdb=" C1 LHG D 407 " pdb=" C3 LHG D 407 " pdb=" O2 LHG D 407 " both_signs ideal model delta sigma weight residual False -2.33 -2.55 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C2 LHG L 101 " pdb=" C1 LHG L 101 " pdb=" C3 LHG L 101 " pdb=" O2 LHG L 101 " both_signs ideal model delta sigma weight residual False -2.33 -2.54 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2806 not shown) Planarity restraints: 3572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO D 411 " 0.110 2.00e-02 2.50e+03 1.04e-01 8.59e+02 pdb=" ND PHO D 411 " 0.049 2.00e-02 2.50e+03 pdb=" C1A PHO D 411 " -0.010 2.00e-02 2.50e+03 pdb=" C1B PHO D 411 " 0.054 2.00e-02 2.50e+03 pdb=" C1C PHO D 411 " 0.023 2.00e-02 2.50e+03 pdb=" C1D PHO D 411 " 0.001 2.00e-02 2.50e+03 pdb=" C2A PHO D 411 " -0.159 2.00e-02 2.50e+03 pdb=" C2B PHO D 411 " -0.092 2.00e-02 2.50e+03 pdb=" C2C PHO D 411 " 0.045 2.00e-02 2.50e+03 pdb=" C2D PHO D 411 " -0.028 2.00e-02 2.50e+03 pdb=" C3A PHO D 411 " 0.257 2.00e-02 2.50e+03 pdb=" C3B PHO D 411 " -0.115 2.00e-02 2.50e+03 pdb=" C3C PHO D 411 " 0.033 2.00e-02 2.50e+03 pdb=" C3D PHO D 411 " -0.042 2.00e-02 2.50e+03 pdb=" C4A PHO D 411 " 0.183 2.00e-02 2.50e+03 pdb=" C4B PHO D 411 " 0.013 2.00e-02 2.50e+03 pdb=" C4C PHO D 411 " -0.003 2.00e-02 2.50e+03 pdb=" C4D PHO D 411 " -0.011 2.00e-02 2.50e+03 pdb=" CAB PHO D 411 " -0.238 2.00e-02 2.50e+03 pdb=" CAC PHO D 411 " 0.045 2.00e-02 2.50e+03 pdb=" CAD PHO D 411 " -0.069 2.00e-02 2.50e+03 pdb=" CBD PHO D 411 " -0.098 2.00e-02 2.50e+03 pdb=" CHA PHO D 411 " -0.038 2.00e-02 2.50e+03 pdb=" CHB PHO D 411 " 0.118 2.00e-02 2.50e+03 pdb=" CHC PHO D 411 " 0.031 2.00e-02 2.50e+03 pdb=" CHD PHO D 411 " -0.027 2.00e-02 2.50e+03 pdb=" CMB PHO D 411 " -0.182 2.00e-02 2.50e+03 pdb=" CMC PHO D 411 " 0.083 2.00e-02 2.50e+03 pdb=" CMD PHO D 411 " -0.044 2.00e-02 2.50e+03 pdb=" NA PHO D 411 " 0.189 2.00e-02 2.50e+03 pdb=" NC PHO D 411 " -0.008 2.00e-02 2.50e+03 pdb=" OBD PHO D 411 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 412 " -0.062 2.00e-02 2.50e+03 9.82e-02 7.71e+02 pdb=" ND PHO D 412 " 0.156 2.00e-02 2.50e+03 pdb=" C1A PHO D 412 " 0.006 2.00e-02 2.50e+03 pdb=" C1B PHO D 412 " -0.041 2.00e-02 2.50e+03 pdb=" C1C PHO D 412 " -0.005 2.00e-02 2.50e+03 pdb=" C1D PHO D 412 " 0.024 2.00e-02 2.50e+03 pdb=" C2A PHO D 412 " 0.240 2.00e-02 2.50e+03 pdb=" C2B PHO D 412 " 0.053 2.00e-02 2.50e+03 pdb=" C2C PHO D 412 " -0.012 2.00e-02 2.50e+03 pdb=" C2D PHO D 412 " 0.005 2.00e-02 2.50e+03 pdb=" C3A PHO D 412 " -0.205 2.00e-02 2.50e+03 pdb=" C3B PHO D 412 " 0.080 2.00e-02 2.50e+03 pdb=" C3C PHO D 412 " -0.038 2.00e-02 2.50e+03 pdb=" C3D PHO D 412 " 0.043 2.00e-02 2.50e+03 pdb=" C4A PHO D 412 " -0.168 2.00e-02 2.50e+03 pdb=" C4B PHO D 412 " 0.008 2.00e-02 2.50e+03 pdb=" C4C PHO D 412 " -0.046 2.00e-02 2.50e+03 pdb=" C4D PHO D 412 " 0.072 2.00e-02 2.50e+03 pdb=" CAB PHO D 412 " 0.160 2.00e-02 2.50e+03 pdb=" CAC PHO D 412 " -0.058 2.00e-02 2.50e+03 pdb=" CAD PHO D 412 " 0.053 2.00e-02 2.50e+03 pdb=" CBD PHO D 412 " -0.073 2.00e-02 2.50e+03 pdb=" CHA PHO D 412 " -0.001 2.00e-02 2.50e+03 pdb=" CHB PHO D 412 " -0.086 2.00e-02 2.50e+03 pdb=" CHC PHO D 412 " 0.008 2.00e-02 2.50e+03 pdb=" CHD PHO D 412 " -0.068 2.00e-02 2.50e+03 pdb=" CMB PHO D 412 " 0.099 2.00e-02 2.50e+03 pdb=" CMC PHO D 412 " 0.003 2.00e-02 2.50e+03 pdb=" CMD PHO D 412 " -0.037 2.00e-02 2.50e+03 pdb=" NA PHO D 412 " -0.224 2.00e-02 2.50e+03 pdb=" NC PHO D 412 " -0.023 2.00e-02 2.50e+03 pdb=" OBD PHO D 412 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CLA B 609 " -0.081 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" ND CLA B 609 " -0.078 2.00e-02 2.50e+03 pdb=" NA CLA B 609 " -0.070 2.00e-02 2.50e+03 pdb=" NC CLA B 609 " -0.067 2.00e-02 2.50e+03 pdb="MG CLA B 609 " 0.297 2.00e-02 2.50e+03 ... (remaining 3569 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 200 2.64 - 3.21: 17734 3.21 - 3.77: 29509 3.77 - 4.34: 41685 4.34 - 4.90: 71220 Nonbonded interactions: 160348 Sorted by model distance: nonbonded pdb=" O ASP D 297 " pdb=" OH TYR D 315 " model vdw 2.080 3.040 nonbonded pdb=" NE2 HIS F 23 " pdb="FE HEM E 101 " model vdw 2.128 3.080 nonbonded pdb=" OH TYR E 19 " pdb=" O THR 1 60 " model vdw 2.184 3.040 nonbonded pdb=" O GLY C 390 " pdb=" ND2 ASN A 298 " model vdw 2.191 3.120 nonbonded pdb=" O ARG B 127 " pdb=" OG1 THR B 128 " model vdw 2.218 3.040 ... (remaining 160343 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.120 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:7.040 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.008 0.178 21061 Z= 0.426 Angle : 1.193 18.453 28997 Z= 0.448 Chirality : 0.040 0.221 2809 Planarity : 0.014 0.149 3572 Dihedral : 18.029 135.215 7567 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.67 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.19), residues: 2063 helix: 2.10 (0.15), residues: 1251 sheet: -0.60 (0.80), residues: 42 loop : -0.69 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 14 TYR 0.009 0.001 TYR D 296 PHE 0.051 0.001 PHE D 185 TRP 0.013 0.001 TRP B 113 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00716 (21032) covalent geometry : angle 1.19282 (28997) hydrogen bonds : bond 0.13241 ( 986) hydrogen bonds : angle 5.47804 ( 2811) Misc. bond : bond 0.06720 ( 29) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.767 Fit side-chains REVERT: B 37 MET cc_start: 0.8157 (mmm) cc_final: 0.7899 (mmt) REVERT: B 175 THR cc_start: 0.8323 (p) cc_final: 0.8085 (p) REVERT: B 256 MET cc_start: 0.8746 (tpp) cc_final: 0.8464 (tpp) REVERT: L 13 LEU cc_start: 0.8690 (tp) cc_final: 0.8470 (tp) outliers start: 0 outliers final: 2 residues processed: 173 average time/residue: 0.5671 time to fit residues: 113.3185 Evaluate side-chains 141 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain A residue 218 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 3.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 32 ASN Z 58 ASN A 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.121214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.099676 restraints weight = 29619.415| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.79 r_work: 0.3221 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.199 21061 Z= 0.131 Angle : 0.611 13.742 28997 Z= 0.276 Chirality : 0.042 0.333 2809 Planarity : 0.005 0.058 3572 Dihedral : 16.339 122.339 4058 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 1.12 % Allowed : 6.76 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.19), residues: 2063 helix: 2.25 (0.15), residues: 1269 sheet: -0.11 (0.91), residues: 32 loop : -0.63 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 14 TYR 0.011 0.001 TYR L 35 PHE 0.015 0.001 PHE D 113 TRP 0.011 0.001 TRP D 21 HIS 0.008 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00259 (21032) covalent geometry : angle 0.61109 (28997) hydrogen bonds : bond 0.05035 ( 986) hydrogen bonds : angle 4.34777 ( 2811) Misc. bond : bond 0.04295 ( 29) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.533 Fit side-chains REVERT: B 256 MET cc_start: 0.8959 (tpp) cc_final: 0.8700 (tpp) REVERT: D 220 ASN cc_start: 0.8585 (m110) cc_final: 0.8269 (m-40) REVERT: I 23 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8456 (m-80) REVERT: C 17 GLU cc_start: 0.8360 (pt0) cc_final: 0.7920 (mp0) REVERT: C 372 ILE cc_start: 0.8135 (mt) cc_final: 0.7621 (mp) REVERT: A 167 SER cc_start: 0.9004 (t) cc_final: 0.8802 (t) outliers start: 19 outliers final: 6 residues processed: 162 average time/residue: 0.5810 time to fit residues: 107.4162 Evaluate side-chains 153 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 105 optimal weight: 0.7980 chunk 93 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 129 GLN V 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.119524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098143 restraints weight = 29659.300| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.81 r_work: 0.3197 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.240 21061 Z= 0.130 Angle : 0.553 9.853 28997 Z= 0.257 Chirality : 0.040 0.313 2809 Planarity : 0.005 0.054 3572 Dihedral : 15.204 121.542 4054 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 1.59 % Allowed : 9.47 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.19), residues: 2063 helix: 2.36 (0.15), residues: 1270 sheet: 0.01 (0.91), residues: 32 loop : -0.65 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 14 TYR 0.009 0.001 TYR E 55 PHE 0.020 0.001 PHE D 113 TRP 0.012 0.001 TRP D 191 HIS 0.006 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00275 (21032) covalent geometry : angle 0.55350 (28997) hydrogen bonds : bond 0.04897 ( 986) hydrogen bonds : angle 4.13729 ( 2811) Misc. bond : bond 0.04598 ( 29) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.650 Fit side-chains REVERT: B 84 THR cc_start: 0.7805 (t) cc_final: 0.7573 (m) REVERT: B 256 MET cc_start: 0.9001 (tpp) cc_final: 0.8609 (tpp) REVERT: D 220 ASN cc_start: 0.8532 (m110) cc_final: 0.8256 (m-40) REVERT: E 80 SER cc_start: 0.9268 (t) cc_final: 0.8954 (m) REVERT: I 1 MET cc_start: 0.7656 (mpp) cc_final: 0.7441 (pmm) REVERT: I 23 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: L 1 MET cc_start: 0.3809 (mmt) cc_final: 0.3055 (mmp) REVERT: C 17 GLU cc_start: 0.8361 (pt0) cc_final: 0.7908 (mp0) REVERT: C 234 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7976 (mp) REVERT: C 456 SER cc_start: 0.7770 (t) cc_final: 0.7563 (t) REVERT: A 59 ASP cc_start: 0.7942 (p0) cc_final: 0.7733 (p0) outliers start: 27 outliers final: 14 residues processed: 161 average time/residue: 0.5720 time to fit residues: 105.8849 Evaluate side-chains 157 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 152 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 143 optimal weight: 0.0980 chunk 170 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN V 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.119539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098147 restraints weight = 29666.835| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.81 r_work: 0.3213 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.166 21061 Z= 0.121 Angle : 0.544 11.024 28997 Z= 0.252 Chirality : 0.040 0.306 2809 Planarity : 0.004 0.055 3572 Dihedral : 14.976 120.271 4054 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Rotamer: Outliers : 1.82 % Allowed : 11.06 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.19), residues: 2063 helix: 2.41 (0.15), residues: 1268 sheet: -0.10 (0.90), residues: 32 loop : -0.67 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 14 TYR 0.014 0.001 TYR E 55 PHE 0.018 0.001 PHE D 113 TRP 0.012 0.001 TRP D 21 HIS 0.005 0.001 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00263 (21032) covalent geometry : angle 0.54418 (28997) hydrogen bonds : bond 0.04710 ( 986) hydrogen bonds : angle 4.05354 ( 2811) Misc. bond : bond 0.03150 ( 29) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.696 Fit side-chains REVERT: B 84 THR cc_start: 0.7919 (t) cc_final: 0.7701 (m) REVERT: B 121 GLU cc_start: 0.7953 (tt0) cc_final: 0.7698 (tt0) REVERT: B 231 MET cc_start: 0.8742 (mtm) cc_final: 0.8367 (mtm) REVERT: B 256 MET cc_start: 0.9014 (tpp) cc_final: 0.8657 (tpp) REVERT: D 24 GLN cc_start: 0.8595 (mt0) cc_final: 0.8216 (tt0) REVERT: D 220 ASN cc_start: 0.8586 (m110) cc_final: 0.8320 (m-40) REVERT: E 69 ARG cc_start: 0.9031 (ttt180) cc_final: 0.8489 (ttt180) REVERT: E 80 SER cc_start: 0.9239 (t) cc_final: 0.8970 (m) REVERT: I 23 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: C 17 GLU cc_start: 0.8367 (pt0) cc_final: 0.7944 (mp0) REVERT: C 456 SER cc_start: 0.7789 (t) cc_final: 0.7586 (m) REVERT: A 64 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7416 (mpt180) REVERT: A 331 MET cc_start: 0.8448 (mmm) cc_final: 0.8063 (tpt) outliers start: 31 outliers final: 12 residues processed: 158 average time/residue: 0.6127 time to fit residues: 110.3804 Evaluate side-chains 162 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 329 MET Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 146 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 99 optimal weight: 0.0030 chunk 197 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 186 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.120256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099007 restraints weight = 29423.633| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.80 r_work: 0.3210 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.242 21061 Z= 0.144 Angle : 0.530 9.721 28997 Z= 0.248 Chirality : 0.039 0.296 2809 Planarity : 0.004 0.056 3572 Dihedral : 14.835 120.096 4054 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.59 % Allowed : 11.59 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.19), residues: 2063 helix: 2.49 (0.15), residues: 1264 sheet: -0.05 (0.90), residues: 32 loop : -0.63 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 29 TYR 0.008 0.001 TYR A 126 PHE 0.017 0.001 PHE D 113 TRP 0.011 0.001 TRP D 21 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00243 (21032) covalent geometry : angle 0.53037 (28997) hydrogen bonds : bond 0.04473 ( 986) hydrogen bonds : angle 3.97628 ( 2811) Misc. bond : bond 0.23065 ( 29) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.666 Fit side-chains REVERT: B 81 SER cc_start: 0.9307 (p) cc_final: 0.8979 (m) REVERT: B 84 THR cc_start: 0.7992 (t) cc_final: 0.7787 (m) REVERT: B 121 GLU cc_start: 0.7956 (tt0) cc_final: 0.7685 (tt0) REVERT: B 231 MET cc_start: 0.8767 (mtm) cc_final: 0.8410 (mtm) REVERT: B 256 MET cc_start: 0.9002 (tpp) cc_final: 0.8656 (tpp) REVERT: D 24 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: D 220 ASN cc_start: 0.8585 (m110) cc_final: 0.8348 (m-40) REVERT: E 69 ARG cc_start: 0.9032 (ttt180) cc_final: 0.8486 (ttt180) REVERT: I 23 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: C 17 GLU cc_start: 0.8393 (pt0) cc_final: 0.7969 (mp0) REVERT: C 456 SER cc_start: 0.7781 (t) cc_final: 0.7577 (m) REVERT: A 83 ILE cc_start: 0.8526 (mp) cc_final: 0.8173 (mp) REVERT: A 331 MET cc_start: 0.8437 (mmm) cc_final: 0.8112 (tpt) outliers start: 27 outliers final: 14 residues processed: 164 average time/residue: 0.6026 time to fit residues: 112.8887 Evaluate side-chains 160 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 329 MET Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 99 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 182 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 HIS F 23 HIS F 40 GLN V 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094640 restraints weight = 29634.816| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.80 r_work: 0.3123 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.111 21061 Z= 0.217 Angle : 0.618 12.428 28997 Z= 0.290 Chirality : 0.043 0.370 2809 Planarity : 0.005 0.058 3572 Dihedral : 15.280 120.944 4054 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.34 % Favored : 96.61 % Rotamer: Outliers : 1.65 % Allowed : 12.29 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.19), residues: 2063 helix: 2.24 (0.15), residues: 1264 sheet: -0.12 (0.93), residues: 32 loop : -0.76 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 14 TYR 0.013 0.002 TYR A 126 PHE 0.021 0.002 PHE D 113 TRP 0.014 0.002 TRP B 247 HIS 0.007 0.001 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00479 (21032) covalent geometry : angle 0.61769 (28997) hydrogen bonds : bond 0.06035 ( 986) hydrogen bonds : angle 4.21287 ( 2811) Misc. bond : bond 0.20671 ( 29) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.673 Fit side-chains REVERT: B 81 SER cc_start: 0.9316 (p) cc_final: 0.9053 (m) REVERT: B 121 GLU cc_start: 0.8057 (tt0) cc_final: 0.7772 (tt0) REVERT: B 256 MET cc_start: 0.9046 (tpp) cc_final: 0.8672 (tpp) REVERT: D 24 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: D 220 ASN cc_start: 0.8600 (m110) cc_final: 0.8366 (m-40) REVERT: E 69 ARG cc_start: 0.9091 (ttt180) cc_final: 0.8543 (ttt180) REVERT: I 23 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8678 (m-80) REVERT: C 17 GLU cc_start: 0.8368 (pt0) cc_final: 0.7962 (mp0) REVERT: C 456 SER cc_start: 0.7852 (t) cc_final: 0.7640 (m) REVERT: A 331 MET cc_start: 0.8584 (mmm) cc_final: 0.8272 (tpt) outliers start: 28 outliers final: 13 residues processed: 164 average time/residue: 0.6387 time to fit residues: 118.8443 Evaluate side-chains 162 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 125 optimal weight: 7.9990 chunk 93 optimal weight: 0.0170 chunk 147 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096521 restraints weight = 29672.146| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.82 r_work: 0.3171 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.819 21061 Z= 0.130 Angle : 0.540 10.477 28997 Z= 0.254 Chirality : 0.040 0.302 2809 Planarity : 0.004 0.058 3572 Dihedral : 14.914 120.755 4054 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 1.76 % Allowed : 13.35 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.19), residues: 2063 helix: 2.45 (0.15), residues: 1257 sheet: -0.07 (0.94), residues: 32 loop : -0.67 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 14 TYR 0.010 0.001 TYR A 126 PHE 0.017 0.001 PHE D 113 TRP 0.013 0.001 TRP B 247 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00251 (21032) covalent geometry : angle 0.53955 (28997) hydrogen bonds : bond 0.04832 ( 986) hydrogen bonds : angle 4.02333 ( 2811) Misc. bond : bond 0.15207 ( 29) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.660 Fit side-chains REVERT: B 81 SER cc_start: 0.9304 (p) cc_final: 0.9054 (m) REVERT: B 121 GLU cc_start: 0.8012 (tt0) cc_final: 0.7713 (tt0) REVERT: B 218 CYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7936 (t) REVERT: B 256 MET cc_start: 0.9039 (tpp) cc_final: 0.8688 (tpp) REVERT: B 467 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7661 (mp) REVERT: D 24 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: D 220 ASN cc_start: 0.8585 (m110) cc_final: 0.8352 (m-40) REVERT: E 69 ARG cc_start: 0.9074 (ttt180) cc_final: 0.8582 (ttt180) REVERT: I 23 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8577 (m-80) REVERT: C 17 GLU cc_start: 0.8376 (pt0) cc_final: 0.7989 (mp0) REVERT: C 72 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8573 (pt0) REVERT: C 456 SER cc_start: 0.7836 (t) cc_final: 0.7626 (m) REVERT: A 64 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.6575 (mtm-85) REVERT: A 331 MET cc_start: 0.8500 (mmm) cc_final: 0.8192 (tpt) outliers start: 30 outliers final: 17 residues processed: 169 average time/residue: 0.6149 time to fit residues: 118.2500 Evaluate side-chains 173 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain 1 residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 118 optimal weight: 6.9990 chunk 146 optimal weight: 0.2980 chunk 95 optimal weight: 0.5980 chunk 152 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN V 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.117904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096643 restraints weight = 29610.387| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.81 r_work: 0.3172 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.650 21061 Z= 0.127 Angle : 0.536 10.767 28997 Z= 0.252 Chirality : 0.039 0.293 2809 Planarity : 0.004 0.058 3572 Dihedral : 14.779 120.535 4054 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 1.41 % Allowed : 14.35 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.19), residues: 2063 helix: 2.42 (0.15), residues: 1265 sheet: -0.04 (0.93), residues: 32 loop : -0.71 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 14 TYR 0.009 0.001 TYR L 35 PHE 0.019 0.001 PHE D 113 TRP 0.014 0.001 TRP D 21 HIS 0.004 0.001 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00260 (21032) covalent geometry : angle 0.53604 (28997) hydrogen bonds : bond 0.04747 ( 986) hydrogen bonds : angle 3.98244 ( 2811) Misc. bond : bond 0.12070 ( 29) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.555 Fit side-chains REVERT: B 81 SER cc_start: 0.9300 (p) cc_final: 0.9078 (m) REVERT: B 121 GLU cc_start: 0.7998 (tt0) cc_final: 0.7691 (tt0) REVERT: B 218 CYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7992 (t) REVERT: B 256 MET cc_start: 0.9026 (tpp) cc_final: 0.8669 (tpp) REVERT: B 467 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7681 (mp) REVERT: D 24 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: D 220 ASN cc_start: 0.8584 (m110) cc_final: 0.8349 (m-40) REVERT: E 69 ARG cc_start: 0.9073 (ttt180) cc_final: 0.8589 (ttt180) REVERT: I 23 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8558 (m-80) REVERT: C 17 GLU cc_start: 0.8388 (pt0) cc_final: 0.8001 (mp0) REVERT: C 273 ILE cc_start: 0.8543 (mt) cc_final: 0.8282 (mp) REVERT: C 456 SER cc_start: 0.7838 (t) cc_final: 0.7635 (m) REVERT: A 331 MET cc_start: 0.8500 (mmm) cc_final: 0.8238 (tpt) outliers start: 24 outliers final: 12 residues processed: 164 average time/residue: 0.5757 time to fit residues: 107.8452 Evaluate side-chains 166 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 158 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN A 76 ASN A 303 ASN A 322 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.093483 restraints weight = 29834.835| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.82 r_work: 0.3105 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.777 21061 Z= 0.212 Angle : 0.612 12.653 28997 Z= 0.287 Chirality : 0.043 0.313 2809 Planarity : 0.005 0.059 3572 Dihedral : 15.095 120.839 4054 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 1.71 % Allowed : 14.24 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.19), residues: 2063 helix: 2.23 (0.15), residues: 1258 sheet: -0.18 (0.95), residues: 32 loop : -0.81 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 14 TYR 0.013 0.002 TYR A 126 PHE 0.025 0.002 PHE D 113 TRP 0.015 0.002 TRP B 247 HIS 0.008 0.001 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00488 (21032) covalent geometry : angle 0.61151 (28997) hydrogen bonds : bond 0.06090 ( 986) hydrogen bonds : angle 4.21576 ( 2811) Misc. bond : bond 0.14458 ( 29) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.700 Fit side-chains REVERT: B 121 GLU cc_start: 0.8099 (tt0) cc_final: 0.7781 (tt0) REVERT: B 256 MET cc_start: 0.9069 (tpp) cc_final: 0.8732 (tpp) REVERT: B 467 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7710 (mp) REVERT: D 24 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: D 220 ASN cc_start: 0.8596 (m110) cc_final: 0.8361 (m-40) REVERT: E 69 ARG cc_start: 0.9091 (ttt180) cc_final: 0.8567 (ttt180) REVERT: I 23 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8688 (m-80) REVERT: C 17 GLU cc_start: 0.8364 (pt0) cc_final: 0.7970 (mp0) REVERT: C 189 ASN cc_start: 0.8581 (m-40) cc_final: 0.8149 (t0) REVERT: C 456 SER cc_start: 0.7890 (t) cc_final: 0.7684 (m) REVERT: A 172 MET cc_start: 0.9043 (ttp) cc_final: 0.8771 (ttt) REVERT: A 331 MET cc_start: 0.8579 (mmm) cc_final: 0.8300 (tpt) outliers start: 29 outliers final: 17 residues processed: 172 average time/residue: 0.5615 time to fit residues: 110.7310 Evaluate side-chains 173 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain 1 residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 191 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN H 69 ASN V 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096270 restraints weight = 29655.097| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.82 r_work: 0.3168 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.596 21061 Z= 0.131 Angle : 0.556 12.747 28997 Z= 0.261 Chirality : 0.040 0.302 2809 Planarity : 0.004 0.059 3572 Dihedral : 14.661 120.525 4054 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.80 % Rotamer: Outliers : 1.24 % Allowed : 14.88 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.19), residues: 2063 helix: 2.39 (0.15), residues: 1259 sheet: -0.08 (0.93), residues: 32 loop : -0.79 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 14 TYR 0.009 0.001 TYR A 126 PHE 0.019 0.001 PHE F 15 TRP 0.014 0.001 TRP B 247 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00277 (21032) covalent geometry : angle 0.55572 (28997) hydrogen bonds : bond 0.04978 ( 986) hydrogen bonds : angle 4.05999 ( 2811) Misc. bond : bond 0.11078 ( 29) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.641 Fit side-chains REVERT: B 55 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8512 (ptm) REVERT: B 256 MET cc_start: 0.9050 (tpp) cc_final: 0.8699 (tpp) REVERT: B 467 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7676 (mp) REVERT: D 24 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: D 220 ASN cc_start: 0.8591 (m110) cc_final: 0.8357 (m-40) REVERT: D 265 ARG cc_start: 0.7400 (ttt-90) cc_final: 0.6583 (ttp-170) REVERT: E 38 VAL cc_start: 0.7934 (t) cc_final: 0.7555 (p) REVERT: E 69 ARG cc_start: 0.9078 (ttt180) cc_final: 0.8589 (ttt180) REVERT: I 23 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8566 (m-80) REVERT: C 17 GLU cc_start: 0.8376 (pt0) cc_final: 0.7992 (mp0) REVERT: C 189 ASN cc_start: 0.8636 (m-40) cc_final: 0.8230 (t0) REVERT: C 273 ILE cc_start: 0.8520 (mt) cc_final: 0.8253 (mp) REVERT: C 456 SER cc_start: 0.7713 (t) cc_final: 0.7503 (m) REVERT: A 172 MET cc_start: 0.9018 (ttp) cc_final: 0.8708 (ttt) REVERT: A 331 MET cc_start: 0.8504 (mmm) cc_final: 0.8213 (tpt) outliers start: 21 outliers final: 13 residues processed: 164 average time/residue: 0.5682 time to fit residues: 106.4167 Evaluate side-chains 169 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain 1 residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 68 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 ASN V 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.116252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095145 restraints weight = 29607.692| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.81 r_work: 0.3164 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.596 21061 Z= 0.137 Angle : 0.548 12.900 28997 Z= 0.259 Chirality : 0.040 0.300 2809 Planarity : 0.005 0.059 3572 Dihedral : 14.648 120.335 4054 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Rotamer: Outliers : 1.29 % Allowed : 14.88 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.19), residues: 2063 helix: 2.38 (0.15), residues: 1259 sheet: -0.09 (0.92), residues: 32 loop : -0.80 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 476 TYR 0.009 0.001 TYR A 126 PHE 0.021 0.001 PHE F 15 TRP 0.013 0.001 TRP B 247 HIS 0.005 0.001 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00294 (21032) covalent geometry : angle 0.54767 (28997) hydrogen bonds : bond 0.05020 ( 986) hydrogen bonds : angle 4.05424 ( 2811) Misc. bond : bond 0.11080 ( 29) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6010.72 seconds wall clock time: 103 minutes 7.42 seconds (6187.42 seconds total)