Starting phenix.real_space_refine on Thu Jan 23 10:49:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zee_60026/01_2025/8zee_60026_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zee_60026/01_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_60026/01_2025/8zee_60026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zee_60026/01_2025/8zee_60026.map" model { file = "/net/cci-nas-00/data/ceres_data/8zee_60026/01_2025/8zee_60026_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zee_60026/01_2025/8zee_60026_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 12.25, per 1000 atoms: 0.61 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: 6.90 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.94 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: 5.19 Time building geometry restraints manager: 7.41 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.310 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.830 ------------------------------------------------------------------------------- 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 : 0.007 0.178 21032 Z= 0.372 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 : 5.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (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 TRP 0.013 0.001 TRP B 113 HIS 0.006 0.001 HIS B 202 PHE 0.051 0.001 PHE D 185 TYR 0.009 0.001 TYR D 296 ARG 0.009 0.000 ARG C 14 *********************** 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 : 1.883 Fit side-chains REVERT: B 37 MET cc_start: 0.8157 (mmm) cc_final: 0.7934 (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: 0.8465 (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: 1.1747 time to fit residues: 235.4575 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 : 1.903 ------------------------------------------------------------------------------- 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 172 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 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 = 0.3632 r_free = 0.3632 target = 0.119893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098448 restraints weight = 29535.131| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.78 r_work: 0.3196 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21032 Z= 0.185 Angle : 0.619 12.700 28997 Z= 0.281 Chirality : 0.043 0.334 2809 Planarity : 0.005 0.057 3572 Dihedral : 16.419 122.029 4058 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 1.24 % Allowed : 6.82 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.19), residues: 2063 helix: 2.21 (0.15), residues: 1268 sheet: -0.10 (0.92), residues: 32 loop : -0.67 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 191 HIS 0.009 0.002 HIS B 201 PHE 0.018 0.001 PHE D 113 TYR 0.010 0.001 TYR L 35 ARG 0.006 0.000 ARG C 14 *********************** 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 176 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.814 Fit side-chains REVERT: B 37 MET cc_start: 0.8530 (mmm) cc_final: 0.8326 (tpt) REVERT: B 84 THR cc_start: 0.7852 (t) cc_final: 0.7608 (m) REVERT: B 256 MET cc_start: 0.8982 (tpp) cc_final: 0.8737 (tpp) REVERT: D 220 ASN cc_start: 0.8593 (m110) cc_final: 0.8278 (m-40) REVERT: I 23 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8515 (m-80) REVERT: C 17 GLU cc_start: 0.8376 (pt0) cc_final: 0.7938 (mp0) REVERT: C 372 ILE cc_start: 0.8155 (mt) cc_final: 0.7700 (mp) REVERT: A 167 SER cc_start: 0.9011 (t) cc_final: 0.8802 (t) outliers start: 21 outliers final: 5 residues processed: 161 average time/residue: 1.2696 time to fit residues: 234.6276 Evaluate side-chains 148 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 9 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 90 optimal weight: 0.0000 chunk 116 optimal weight: 7.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 HIS F 40 GLN V 32 ASN A 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.092730 restraints weight = 29573.133| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.79 r_work: 0.3112 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21032 Z= 0.313 Angle : 0.644 12.216 28997 Z= 0.299 Chirality : 0.044 0.332 2809 Planarity : 0.006 0.058 3572 Dihedral : 15.923 122.160 4054 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 1.71 % Allowed : 10.18 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.19), residues: 2063 helix: 2.03 (0.15), residues: 1269 sheet: -0.06 (0.94), residues: 32 loop : -0.84 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 247 HIS 0.009 0.002 HIS C 429 PHE 0.025 0.002 PHE D 113 TYR 0.013 0.002 TYR D 244 ARG 0.007 0.000 ARG C 14 *********************** 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: 29 poor density : 154 time to evaluate : 2.008 Fit side-chains REVERT: B 84 THR cc_start: 0.8239 (t) cc_final: 0.8031 (m) REVERT: B 256 MET cc_start: 0.9067 (tpp) cc_final: 0.8630 (tpp) REVERT: D 220 ASN cc_start: 0.8637 (m110) cc_final: 0.8379 (m-40) REVERT: E 69 ARG cc_start: 0.9061 (ttt180) cc_final: 0.8491 (ttt180) REVERT: I 23 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8716 (m-80) REVERT: C 17 GLU cc_start: 0.8352 (pt0) cc_final: 0.7906 (mp0) REVERT: C 234 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7881 (mp) REVERT: C 456 SER cc_start: 0.7921 (t) cc_final: 0.7704 (m) REVERT: A 16 ARG cc_start: 0.6201 (tmt170) cc_final: 0.5918 (tmt170) REVERT: A 266 ASN cc_start: 0.7788 (t0) cc_final: 0.7579 (t160) outliers start: 29 outliers final: 17 residues processed: 162 average time/residue: 1.3589 time to fit residues: 251.4279 Evaluate side-chains 163 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 MET 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 125 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 17 optimal weight: 0.0070 chunk 79 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 32 optimal weight: 0.0060 chunk 97 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 overall best weight: 0.5214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 69 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 = 0.3602 r_free = 0.3602 target = 0.117628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096477 restraints weight = 29600.250| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.79 r_work: 0.3187 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21032 Z= 0.154 Angle : 0.546 10.305 28997 Z= 0.255 Chirality : 0.040 0.316 2809 Planarity : 0.004 0.058 3572 Dihedral : 15.332 120.395 4054 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.88 % Allowed : 11.71 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.19), residues: 2063 helix: 2.32 (0.15), residues: 1266 sheet: -0.17 (0.91), residues: 32 loop : -0.80 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 347 HIS 0.005 0.001 HIS C 418 PHE 0.016 0.001 PHE D 113 TYR 0.010 0.001 TYR A 254 ARG 0.004 0.000 ARG C 14 *********************** 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 191 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.898 Fit side-chains REVERT: B 81 SER cc_start: 0.9314 (p) cc_final: 0.9010 (m) REVERT: B 256 MET cc_start: 0.9021 (tpp) cc_final: 0.8669 (tpp) REVERT: D 24 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: D 220 ASN cc_start: 0.8609 (m110) cc_final: 0.8352 (m-40) REVERT: E 69 ARG cc_start: 0.9038 (ttt180) cc_final: 0.8556 (ttt180) REVERT: E 80 SER cc_start: 0.9258 (t) cc_final: 0.8965 (m) REVERT: I 1 MET cc_start: 0.8514 (pmm) cc_final: 0.7943 (pmm) REVERT: I 23 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8532 (m-80) REVERT: C 17 GLU cc_start: 0.8411 (pt0) cc_final: 0.7974 (mp0) REVERT: C 168 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8117 (mtp) REVERT: C 456 SER cc_start: 0.7858 (t) cc_final: 0.7655 (m) REVERT: A 266 ASN cc_start: 0.7688 (t0) cc_final: 0.7462 (t160) REVERT: A 331 MET cc_start: 0.8488 (mmm) cc_final: 0.8147 (tpt) outliers start: 32 outliers final: 13 residues processed: 168 average time/residue: 1.2323 time to fit residues: 238.5096 Evaluate side-chains 165 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.993 ------------------------------------------------------------------------------- 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 237 VAL 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 213 ILE Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 115 optimal weight: 5.9990 chunk 94 optimal weight: 0.0570 chunk 122 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 39 optimal weight: 0.0370 chunk 107 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 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 = 0.3608 r_free = 0.3608 target = 0.118130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096929 restraints weight = 29687.302| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.80 r_work: 0.3179 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21032 Z= 0.160 Angle : 0.539 10.231 28997 Z= 0.250 Chirality : 0.039 0.302 2809 Planarity : 0.004 0.058 3572 Dihedral : 14.972 119.853 4054 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 2.12 % Allowed : 12.18 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.19), residues: 2063 helix: 2.47 (0.15), residues: 1257 sheet: -0.10 (0.92), residues: 32 loop : -0.70 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 21 HIS 0.004 0.001 HIS C 429 PHE 0.019 0.001 PHE D 113 TYR 0.013 0.001 TYR E 55 ARG 0.006 0.000 ARG C 14 *********************** 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 193 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.839 Fit side-chains REVERT: B 81 SER cc_start: 0.9304 (p) cc_final: 0.9027 (m) REVERT: B 121 GLU cc_start: 0.7999 (tt0) cc_final: 0.7702 (tt0) REVERT: B 218 CYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7705 (t) REVERT: B 256 MET cc_start: 0.9006 (tpp) cc_final: 0.8633 (tpp) REVERT: B 422 ARG cc_start: 0.8813 (ttm110) cc_final: 0.8541 (ttm110) REVERT: D 24 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: D 126 MET cc_start: 0.8529 (ttt) cc_final: 0.8325 (tpp) REVERT: D 220 ASN cc_start: 0.8575 (m110) cc_final: 0.8338 (m-40) REVERT: D 265 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6435 (ttp-170) REVERT: E 69 ARG cc_start: 0.9064 (ttt180) cc_final: 0.8551 (ttt180) REVERT: I 1 MET cc_start: 0.8590 (pmm) cc_final: 0.8050 (pmm) REVERT: I 23 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: C 17 GLU cc_start: 0.8394 (pt0) cc_final: 0.7994 (mp0) REVERT: C 168 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8060 (mtp) REVERT: A 266 ASN cc_start: 0.7654 (t0) cc_final: 0.7446 (t160) REVERT: A 331 MET cc_start: 0.8496 (mmm) cc_final: 0.8273 (tpt) outliers start: 36 outliers final: 13 residues processed: 169 average time/residue: 1.3142 time to fit residues: 254.0296 Evaluate side-chains 165 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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 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 D residue 265 ARG Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 120 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 HIS V 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093275 restraints weight = 29866.702| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.82 r_work: 0.3103 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21032 Z= 0.291 Angle : 0.604 12.491 28997 Z= 0.283 Chirality : 0.042 0.321 2809 Planarity : 0.005 0.059 3572 Dihedral : 15.247 121.613 4054 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 1.71 % Allowed : 13.82 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 2063 helix: 2.23 (0.15), residues: 1258 sheet: -0.15 (0.96), residues: 32 loop : -0.79 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 247 HIS 0.007 0.001 HIS C 429 PHE 0.023 0.002 PHE D 113 TYR 0.013 0.002 TYR A 126 ARG 0.006 0.000 ARG C 14 *********************** 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 188 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.852 Fit side-chains REVERT: B 81 SER cc_start: 0.9314 (p) cc_final: 0.9101 (m) REVERT: B 121 GLU cc_start: 0.8125 (tt0) cc_final: 0.7800 (tt0) REVERT: B 256 MET cc_start: 0.9053 (tpp) cc_final: 0.8671 (tpp) REVERT: B 422 ARG cc_start: 0.8832 (ttm110) cc_final: 0.8565 (ttm110) REVERT: D 24 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: D 220 ASN cc_start: 0.8597 (m110) cc_final: 0.8361 (m-40) REVERT: D 265 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6919 (ttp-170) REVERT: E 69 ARG cc_start: 0.9091 (ttt180) cc_final: 0.8539 (ttt180) REVERT: H 79 MET cc_start: 0.8298 (mmm) cc_final: 0.8085 (tpp) REVERT: I 1 MET cc_start: 0.8762 (pmm) cc_final: 0.8167 (pmm) REVERT: I 23 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8672 (m-80) REVERT: C 17 GLU cc_start: 0.8292 (pt0) cc_final: 0.7983 (mp0) REVERT: C 72 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8702 (pt0) REVERT: C 330 MET cc_start: 0.8213 (ptm) cc_final: 0.8007 (ptm) REVERT: A 331 MET cc_start: 0.8569 (mmm) cc_final: 0.8254 (tpt) outliers start: 29 outliers final: 19 residues processed: 172 average time/residue: 1.3779 time to fit residues: 270.1454 Evaluate side-chains 176 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 D residue 24 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 385 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN V 32 ASN A 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.113918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.092876 restraints weight = 29780.673| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.80 r_work: 0.3095 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21032 Z= 0.304 Angle : 0.602 11.776 28997 Z= 0.284 Chirality : 0.042 0.321 2809 Planarity : 0.005 0.061 3572 Dihedral : 15.274 120.953 4054 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 2.35 % Allowed : 14.24 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2063 helix: 2.12 (0.15), residues: 1258 sheet: -0.19 (0.96), residues: 32 loop : -0.90 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 247 HIS 0.007 0.001 HIS C 429 PHE 0.028 0.002 PHE D 113 TYR 0.014 0.002 TYR A 126 ARG 0.007 0.000 ARG C 14 *********************** 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 198 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.849 Fit side-chains REVERT: B 256 MET cc_start: 0.9066 (tpp) cc_final: 0.8657 (tpp) REVERT: B 422 ARG cc_start: 0.8836 (ttm110) cc_final: 0.8568 (ttm110) REVERT: D 14 TRP cc_start: 0.7919 (t60) cc_final: 0.7642 (t60) REVERT: D 24 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: D 220 ASN cc_start: 0.8609 (m110) cc_final: 0.8384 (m-40) REVERT: D 265 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6735 (ttp-170) REVERT: E 69 ARG cc_start: 0.9098 (ttt180) cc_final: 0.8570 (ttt180) REVERT: I 1 MET cc_start: 0.8808 (pmm) cc_final: 0.8319 (pmm) REVERT: I 23 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8660 (m-80) REVERT: C 17 GLU cc_start: 0.8313 (pt0) cc_final: 0.7989 (mp0) REVERT: C 72 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8682 (pt0) REVERT: C 168 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8334 (mtp) REVERT: C 330 MET cc_start: 0.8166 (ptm) cc_final: 0.7939 (ptm) REVERT: A 37 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7782 (ptm) REVERT: A 331 MET cc_start: 0.8577 (mmm) cc_final: 0.8311 (tpt) outliers start: 40 outliers final: 20 residues processed: 179 average time/residue: 1.3411 time to fit residues: 277.5253 Evaluate side-chains 180 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 55 MET 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 D residue 24 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 214 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 194 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.113181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092140 restraints weight = 30010.848| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.80 r_work: 0.3103 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21032 Z= 0.264 Angle : 0.587 11.723 28997 Z= 0.277 Chirality : 0.042 0.318 2809 Planarity : 0.005 0.061 3572 Dihedral : 15.212 120.854 4054 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.88 % Allowed : 14.88 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.19), residues: 2063 helix: 2.14 (0.15), residues: 1258 sheet: -0.21 (0.97), residues: 32 loop : -0.91 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 247 HIS 0.006 0.001 HIS C 429 PHE 0.025 0.001 PHE D 113 TYR 0.012 0.001 TYR A 126 ARG 0.007 0.000 ARG C 14 *********************** 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 187 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.793 Fit side-chains REVERT: B 256 MET cc_start: 0.9056 (tpp) cc_final: 0.8655 (tpp) REVERT: B 422 ARG cc_start: 0.8769 (ttm110) cc_final: 0.8557 (ttm110) REVERT: D 14 TRP cc_start: 0.7943 (t60) cc_final: 0.7649 (t60) REVERT: D 24 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: D 220 ASN cc_start: 0.8589 (m110) cc_final: 0.8363 (m-40) REVERT: D 265 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6714 (ttp-170) REVERT: E 69 ARG cc_start: 0.9079 (ttt180) cc_final: 0.8584 (ttt180) REVERT: I 1 MET cc_start: 0.8776 (pmm) cc_final: 0.8358 (pmm) REVERT: I 23 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8663 (m-80) REVERT: C 17 GLU cc_start: 0.8334 (pt0) cc_final: 0.7989 (mp0) REVERT: C 72 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: C 168 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8265 (mtp) REVERT: C 330 MET cc_start: 0.8109 (ptm) cc_final: 0.7904 (ptm) REVERT: A 331 MET cc_start: 0.8563 (mmm) cc_final: 0.8296 (tpt) outliers start: 32 outliers final: 21 residues processed: 169 average time/residue: 1.3328 time to fit residues: 256.2441 Evaluate side-chains 177 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 55 MET 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 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 THR 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 D residue 265 ARG Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 165 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 138 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.116004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.095065 restraints weight = 29583.443| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.80 r_work: 0.3166 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21032 Z= 0.163 Angle : 0.535 10.263 28997 Z= 0.254 Chirality : 0.040 0.303 2809 Planarity : 0.004 0.061 3572 Dihedral : 14.840 120.183 4054 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 1.47 % Allowed : 15.59 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 2063 helix: 2.35 (0.15), residues: 1263 sheet: -0.09 (0.95), residues: 32 loop : -0.83 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 21 HIS 0.004 0.001 HIS B 157 PHE 0.017 0.001 PHE D 113 TYR 0.010 0.001 TYR A 254 ARG 0.009 0.000 ARG B 476 *********************** 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 182 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 2.146 Fit side-chains REVERT: B 41 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8082 (mt-10) REVERT: B 55 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8445 (ptm) REVERT: B 256 MET cc_start: 0.9020 (tpp) cc_final: 0.8646 (tpp) REVERT: B 422 ARG cc_start: 0.8746 (ttm110) cc_final: 0.8523 (ttm110) REVERT: D 14 TRP cc_start: 0.7874 (t60) cc_final: 0.7546 (t60) REVERT: D 24 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: D 220 ASN cc_start: 0.8574 (m110) cc_final: 0.8340 (m-40) REVERT: D 265 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6540 (ttp-170) REVERT: E 69 ARG cc_start: 0.9068 (ttt180) cc_final: 0.8618 (ttt180) REVERT: I 1 MET cc_start: 0.8704 (pmm) cc_final: 0.8204 (pmm) REVERT: I 23 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: C 17 GLU cc_start: 0.8367 (pt0) cc_final: 0.8052 (mp0) REVERT: C 72 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8586 (pt0) REVERT: C 168 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8064 (mtp) REVERT: C 273 ILE cc_start: 0.8522 (mt) cc_final: 0.8254 (mp) REVERT: C 330 MET cc_start: 0.8085 (ptm) cc_final: 0.7876 (ptm) REVERT: A 331 MET cc_start: 0.8477 (mmm) cc_final: 0.8268 (mmt) outliers start: 25 outliers final: 12 residues processed: 169 average time/residue: 1.2916 time to fit residues: 249.8875 Evaluate side-chains 169 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 THR 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 D residue 265 ARG Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 168 MET 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 114 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 189 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 ASN F 40 GLN V 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.094325 restraints weight = 29620.362| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.80 r_work: 0.3150 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21032 Z= 0.193 Angle : 0.544 10.359 28997 Z= 0.258 Chirality : 0.040 0.299 2809 Planarity : 0.005 0.061 3572 Dihedral : 14.768 120.091 4054 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.29 % Allowed : 16.00 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.19), residues: 2063 helix: 2.34 (0.15), residues: 1264 sheet: -0.12 (0.95), residues: 32 loop : -0.84 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 247 HIS 0.005 0.001 HIS B 157 PHE 0.024 0.001 PHE D 113 TYR 0.009 0.001 TYR A 126 ARG 0.009 0.000 ARG B 476 ********************** 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: 22 poor density : 153 time to evaluate : 1.849 Fit side-chains REVERT: B 41 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8064 (mt-10) REVERT: B 55 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8515 (ptm) REVERT: B 256 MET cc_start: 0.9027 (tpp) cc_final: 0.8675 (tpp) REVERT: D 14 TRP cc_start: 0.7897 (t60) cc_final: 0.7618 (t60) REVERT: D 24 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: D 220 ASN cc_start: 0.8563 (m110) cc_final: 0.8324 (m-40) REVERT: D 265 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6501 (ttp-170) REVERT: E 69 ARG cc_start: 0.9076 (ttt180) cc_final: 0.8623 (ttt180) REVERT: I 1 MET cc_start: 0.8718 (pmm) cc_final: 0.8215 (pmm) REVERT: I 23 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: C 17 GLU cc_start: 0.8357 (pt0) cc_final: 0.8024 (mp0) REVERT: C 72 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8574 (pt0) REVERT: C 168 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8103 (mtp) REVERT: C 273 ILE cc_start: 0.8555 (mt) cc_final: 0.8285 (mp) REVERT: C 330 MET cc_start: 0.8066 (ptm) cc_final: 0.7843 (ptm) REVERT: A 331 MET cc_start: 0.8496 (mmm) cc_final: 0.8289 (mmt) outliers start: 22 outliers final: 13 residues processed: 164 average time/residue: 1.3571 time to fit residues: 254.1779 Evaluate side-chains 170 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 THR 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 D residue 265 ARG Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 168 MET 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 1 residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 193 optimal weight: 0.0770 chunk 192 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.116207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095257 restraints weight = 29845.770| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.80 r_work: 0.3166 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21032 Z= 0.166 Angle : 0.532 10.113 28997 Z= 0.253 Chirality : 0.040 0.291 2809 Planarity : 0.005 0.061 3572 Dihedral : 14.604 120.046 4054 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.29 % Allowed : 16.18 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 2063 helix: 2.42 (0.15), residues: 1257 sheet: -0.11 (0.95), residues: 32 loop : -0.81 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 21 HIS 0.004 0.001 HIS B 157 PHE 0.019 0.001 PHE D 113 TYR 0.009 0.001 TYR A 254 ARG 0.009 0.000 ARG B 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11425.96 seconds wall clock time: 203 minutes 27.08 seconds (12207.08 seconds total)