Starting phenix.real_space_refine on Tue Jun 17 15:33:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zee_60026/06_2025/8zee_60026_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zee_60026/06_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_60026/06_2025/8zee_60026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zee_60026/06_2025/8zee_60026.map" model { file = "/net/cci-nas-00/data/ceres_data/8zee_60026/06_2025/8zee_60026_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zee_60026/06_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-5710/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: 12.32, 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: 7.13 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: 1.82 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: 5.51 Time building geometry restraints manager: 7.82 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: 0.640 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: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 45.800 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 61.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.178 21061 Z= 0.426 Angle : 1.193 18.453 28997 Z= 0.448 Chirality : 0.040 0.221 2809 Planarity : 0.014 0.149 3572 Dihedral : 18.029 135.215 7567 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 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 Details of bonding type rmsd hydrogen bonds : bond 0.13241 ( 986) hydrogen bonds : angle 5.47804 ( 2811) covalent geometry : bond 0.00716 (21032) covalent geometry : angle 1.19282 (28997) Misc. bond : bond 0.06720 ( 29) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.912 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: 1.1499 time to fit residues: 230.1602 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 : 1.735 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098430 restraints weight = 29535.275| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.79 r_work: 0.3199 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 0.210 21061 Z= 0.138 Angle : 0.619 12.700 28997 Z= 0.281 Chirality : 0.043 0.334 2809 Planarity : 0.005 0.057 3572 Dihedral : 16.419 122.030 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 Details of bonding type rmsd hydrogen bonds : bond 0.05248 ( 986) hydrogen bonds : angle 4.37404 ( 2811) covalent geometry : bond 0.00292 (21032) covalent geometry : angle 0.61936 (28997) Misc. bond : bond 0.04415 ( 29) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.857 Fit side-chains REVERT: B 37 MET cc_start: 0.8533 (mmm) cc_final: 0.8326 (tpt) REVERT: B 84 THR cc_start: 0.7853 (t) cc_final: 0.7609 (m) REVERT: B 256 MET cc_start: 0.8979 (tpp) cc_final: 0.8734 (tpp) REVERT: D 220 ASN cc_start: 0.8595 (m110) cc_final: 0.8284 (m-40) REVERT: I 23 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: C 17 GLU cc_start: 0.8382 (pt0) cc_final: 0.7944 (mp0) REVERT: C 372 ILE cc_start: 0.8159 (mt) cc_final: 0.7702 (mp) REVERT: A 167 SER cc_start: 0.9001 (t) cc_final: 0.8798 (t) outliers start: 21 outliers final: 5 residues processed: 161 average time/residue: 1.2924 time to fit residues: 238.2124 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 : 2.202 ------------------------------------------------------------------------------- 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: 0.3980 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: 3.9990 chunk 19 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 90 optimal weight: 0.0070 chunk 116 optimal weight: 3.9990 overall best weight: 1.4804 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094284 restraints weight = 29533.055| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.79 r_work: 0.3141 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 21061 Z= 0.180 Angle : 0.607 11.306 28997 Z= 0.282 Chirality : 0.042 0.329 2809 Planarity : 0.005 0.056 3572 Dihedral : 15.699 122.225 4054 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 1.76 % Allowed : 9.65 % Favored : 88.59 % 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: 1.61 (0.19), residues: 2063 helix: 2.13 (0.15), residues: 1271 sheet: 0.01 (0.93), residues: 32 loop : -0.76 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 247 HIS 0.008 0.002 HIS C 429 PHE 0.023 0.002 PHE D 113 TYR 0.013 0.002 TYR D 244 ARG 0.007 0.000 ARG C 14 Details of bonding type rmsd hydrogen bonds : bond 0.05919 ( 986) hydrogen bonds : angle 4.31983 ( 2811) covalent geometry : bond 0.00418 (21032) covalent geometry : angle 0.60683 (28997) Misc. bond : bond 0.04190 ( 29) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.899 Fit side-chains REVERT: B 37 MET cc_start: 0.8585 (mmm) cc_final: 0.8363 (mmt) REVERT: B 84 THR cc_start: 0.8148 (t) cc_final: 0.7938 (m) REVERT: B 256 MET cc_start: 0.9056 (tpp) cc_final: 0.8779 (tpp) REVERT: D 220 ASN cc_start: 0.8631 (m110) cc_final: 0.8364 (m-40) REVERT: I 23 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8636 (m-80) REVERT: C 17 GLU cc_start: 0.8353 (pt0) cc_final: 0.7906 (mp0) REVERT: C 234 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7869 (mp) REVERT: C 456 SER cc_start: 0.7882 (t) cc_final: 0.7661 (m) REVERT: A 16 ARG cc_start: 0.6111 (tmt170) cc_final: 0.5848 (tmt170) REVERT: A 59 ASP cc_start: 0.8126 (p0) cc_final: 0.7922 (p0) REVERT: A 266 ASN cc_start: 0.7762 (t0) cc_final: 0.7555 (t160) outliers start: 30 outliers final: 17 residues processed: 163 average time/residue: 1.2719 time to fit residues: 237.6708 Evaluate side-chains 166 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 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 63 ILE 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: 2.9990 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 17 optimal weight: 0.1980 chunk 79 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.117634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096406 restraints weight = 29606.312| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.80 r_work: 0.3170 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.234 21061 Z= 0.125 Angle : 0.549 10.464 28997 Z= 0.256 Chirality : 0.040 0.314 2809 Planarity : 0.005 0.057 3572 Dihedral : 15.291 120.015 4054 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 1.94 % Allowed : 11.41 % Favored : 86.65 % 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: 1.79 (0.19), residues: 2063 helix: 2.34 (0.15), residues: 1267 sheet: -0.11 (0.92), residues: 32 loop : -0.78 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.005 0.001 HIS C 429 PHE 0.020 0.001 PHE D 113 TYR 0.013 0.001 TYR E 55 ARG 0.006 0.000 ARG C 14 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 986) hydrogen bonds : angle 4.12530 ( 2811) covalent geometry : bond 0.00271 (21032) covalent geometry : angle 0.54898 (28997) Misc. bond : bond 0.04365 ( 29) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 2.109 Fit side-chains REVERT: B 81 SER cc_start: 0.9303 (p) cc_final: 0.9011 (m) REVERT: B 256 MET cc_start: 0.9021 (tpp) cc_final: 0.8650 (tpp) REVERT: D 24 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: D 220 ASN cc_start: 0.8603 (m110) cc_final: 0.8347 (m-40) REVERT: D 265 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6409 (ttp-170) REVERT: E 69 ARG cc_start: 0.9041 (ttt180) cc_final: 0.8563 (ttt180) REVERT: E 80 SER cc_start: 0.9237 (t) cc_final: 0.8963 (m) REVERT: I 1 MET cc_start: 0.8507 (pmm) cc_final: 0.7989 (pmm) REVERT: I 23 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8518 (m-80) REVERT: C 17 GLU cc_start: 0.8385 (pt0) cc_final: 0.7950 (mp0) REVERT: C 168 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8120 (mtp) REVERT: C 456 SER cc_start: 0.7857 (t) cc_final: 0.7653 (m) REVERT: A 59 ASP cc_start: 0.8248 (p0) cc_final: 0.8028 (p0) REVERT: A 266 ASN cc_start: 0.7676 (t0) cc_final: 0.7466 (t160) REVERT: A 331 MET cc_start: 0.8495 (mmm) cc_final: 0.8195 (tpt) outliers start: 33 outliers final: 13 residues processed: 163 average time/residue: 1.6044 time to fit residues: 299.8507 Evaluate side-chains 164 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 2.362 ------------------------------------------------------------------------------- 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 246 PHE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain D residue 24 GLN 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 I residue 24 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 63 ILE 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: 4.9990 chunk 122 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN H 69 ASN V 32 ASN A 303 ASN A 322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095069 restraints weight = 29756.223| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.80 r_work: 0.3149 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.207 21061 Z= 0.142 Angle : 0.559 11.467 28997 Z= 0.260 Chirality : 0.040 0.312 2809 Planarity : 0.005 0.058 3572 Dihedral : 15.145 120.478 4054 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Rotamer: Outliers : 2.06 % Allowed : 12.06 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.38 (0.15), residues: 1257 sheet: -0.12 (0.92), residues: 32 loop : -0.73 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.006 0.001 HIS C 429 PHE 0.025 0.001 PHE D 113 TYR 0.010 0.001 TYR A 126 ARG 0.005 0.000 ARG C 14 Details of bonding type rmsd hydrogen bonds : bond 0.05216 ( 986) hydrogen bonds : angle 4.10075 ( 2811) covalent geometry : bond 0.00319 (21032) covalent geometry : angle 0.55863 (28997) Misc. bond : bond 0.03872 ( 29) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 1.816 Fit side-chains REVERT: B 81 SER cc_start: 0.9298 (p) cc_final: 0.9049 (m) REVERT: B 121 GLU cc_start: 0.8068 (tt0) cc_final: 0.7767 (tt0) REVERT: B 256 MET cc_start: 0.9033 (tpp) cc_final: 0.8670 (tpp) REVERT: D 24 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: D 220 ASN cc_start: 0.8584 (m110) cc_final: 0.8354 (m-40) REVERT: D 265 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6696 (ttp-170) REVERT: E 69 ARG cc_start: 0.9066 (ttt180) cc_final: 0.8544 (ttt180) REVERT: E 80 SER cc_start: 0.9074 (t) cc_final: 0.8809 (m) REVERT: I 1 MET cc_start: 0.8615 (pmm) cc_final: 0.8015 (pmm) REVERT: I 23 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: C 17 GLU cc_start: 0.8378 (pt0) cc_final: 0.7980 (mp0) REVERT: C 456 SER cc_start: 0.7818 (t) cc_final: 0.7612 (m) REVERT: A 64 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.6576 (mtm-85) REVERT: A 266 ASN cc_start: 0.7687 (t0) cc_final: 0.7470 (t160) REVERT: A 331 MET cc_start: 0.8529 (mmm) cc_final: 0.8173 (tpt) outliers start: 35 outliers final: 15 residues processed: 171 average time/residue: 1.6252 time to fit residues: 319.7686 Evaluate side-chains 168 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain 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 385 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain 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: 6.9990 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.115354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.094067 restraints weight = 29782.590| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.80 r_work: 0.3135 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 21061 Z= 0.159 Angle : 0.566 11.504 28997 Z= 0.264 Chirality : 0.041 0.311 2809 Planarity : 0.005 0.059 3572 Dihedral : 15.120 120.978 4054 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Rotamer: Outliers : 1.88 % Allowed : 13.18 % Favored : 84.94 % 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: 1.78 (0.19), residues: 2063 helix: 2.34 (0.15), residues: 1258 sheet: -0.19 (0.94), residues: 32 loop : -0.76 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 247 HIS 0.006 0.001 HIS C 429 PHE 0.023 0.001 PHE D 113 TYR 0.011 0.001 TYR A 126 ARG 0.006 0.000 ARG C 14 Details of bonding type rmsd hydrogen bonds : bond 0.05424 ( 986) hydrogen bonds : angle 4.13538 ( 2811) covalent geometry : bond 0.00367 (21032) covalent geometry : angle 0.56589 (28997) Misc. bond : bond 0.03987 ( 29) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 3.992 Fit side-chains REVERT: B 81 SER cc_start: 0.9313 (p) cc_final: 0.9078 (m) REVERT: B 121 GLU cc_start: 0.8081 (tt0) cc_final: 0.7774 (tt0) REVERT: B 256 MET cc_start: 0.9048 (tpp) cc_final: 0.8658 (tpp) REVERT: B 422 ARG cc_start: 0.8825 (ttm110) cc_final: 0.8565 (ttm110) REVERT: D 24 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: D 220 ASN cc_start: 0.8592 (m110) cc_final: 0.8360 (m-40) REVERT: D 265 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6604 (ttp-170) REVERT: E 69 ARG cc_start: 0.9076 (ttt180) cc_final: 0.8561 (ttt180) REVERT: I 1 MET cc_start: 0.8703 (pmm) cc_final: 0.8034 (pmm) REVERT: I 23 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: C 17 GLU cc_start: 0.8402 (pt0) cc_final: 0.7997 (mp0) REVERT: C 72 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8655 (pt0) REVERT: C 456 SER cc_start: 0.7858 (t) cc_final: 0.7645 (m) REVERT: A 331 MET cc_start: 0.8534 (mmm) cc_final: 0.8334 (tpt) outliers start: 32 outliers final: 22 residues processed: 161 average time/residue: 1.8564 time to fit residues: 342.5987 Evaluate side-chains 174 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 2.386 ------------------------------------------------------------------------------- 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 439 SER Chi-restraints excluded: chain B residue 440 ASP 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 187 ILE 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 63 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 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: 5.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 70 optimal weight: 0.0970 chunk 86 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN V 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095372 restraints weight = 29600.639| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.79 r_work: 0.3168 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 21061 Z= 0.130 Angle : 0.536 11.008 28997 Z= 0.252 Chirality : 0.040 0.302 2809 Planarity : 0.004 0.059 3572 Dihedral : 14.894 120.653 4054 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.80 % Rotamer: Outliers : 2.06 % Allowed : 14.00 % Favored : 83.94 % 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: 1.89 (0.19), residues: 2063 helix: 2.44 (0.15), residues: 1258 sheet: -0.18 (0.94), residues: 32 loop : -0.73 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.005 0.001 HIS C 429 PHE 0.023 0.001 PHE D 113 TYR 0.010 0.001 TYR A 126 ARG 0.008 0.000 ARG C 14 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 986) hydrogen bonds : angle 4.03952 ( 2811) covalent geometry : bond 0.00289 (21032) covalent geometry : angle 0.53599 (28997) Misc. bond : bond 0.03657 ( 29) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 2.158 Fit side-chains REVERT: B 121 GLU cc_start: 0.8046 (tt0) cc_final: 0.7733 (tt0) REVERT: B 218 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8185 (t) REVERT: B 256 MET cc_start: 0.9046 (tpp) cc_final: 0.8699 (tpp) REVERT: B 422 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8550 (ttm110) REVERT: B 467 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7670 (mp) REVERT: D 24 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: D 220 ASN cc_start: 0.8568 (m110) cc_final: 0.8330 (m-40) REVERT: E 69 ARG cc_start: 0.9080 (ttt180) cc_final: 0.8498 (ttt180) REVERT: I 1 MET cc_start: 0.8691 (pmm) cc_final: 0.7978 (pmm) REVERT: I 23 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: C 17 GLU cc_start: 0.8296 (pt0) cc_final: 0.7985 (mp0) REVERT: C 72 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8605 (pt0) REVERT: C 168 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8033 (mtp) REVERT: C 456 SER cc_start: 0.7837 (t) cc_final: 0.7626 (m) REVERT: A 331 MET cc_start: 0.8489 (mmm) cc_final: 0.8234 (tpt) outliers start: 35 outliers final: 18 residues processed: 171 average time/residue: 1.9284 time to fit residues: 383.4054 Evaluate side-chains 175 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain H residue 73 ILE 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 C residue 444 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 63 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 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: 0.8980 chunk 143 optimal weight: 0.0070 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 32 ASN A 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.093999 restraints weight = 29944.702| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.81 r_work: 0.3149 rms_B_bonded: 2.60 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: 0.8181 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.278 21061 Z= 0.151 Angle : 0.555 11.067 28997 Z= 0.261 Chirality : 0.040 0.304 2809 Planarity : 0.005 0.059 3572 Dihedral : 14.841 120.413 4054 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 2.35 % Allowed : 14.18 % Favored : 83.47 % 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: 1.82 (0.19), residues: 2063 helix: 2.38 (0.15), residues: 1259 sheet: -0.30 (0.93), residues: 32 loop : -0.77 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 247 HIS 0.006 0.001 HIS C 429 PHE 0.022 0.001 PHE D 113 TYR 0.011 0.001 TYR A 126 ARG 0.007 0.000 ARG C 14 Details of bonding type rmsd hydrogen bonds : bond 0.05313 ( 986) hydrogen bonds : angle 4.08671 ( 2811) covalent geometry : bond 0.00344 (21032) covalent geometry : angle 0.55467 (28997) Misc. bond : bond 0.05190 ( 29) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 2.135 Fit side-chains REVERT: B 121 GLU cc_start: 0.8051 (tt0) cc_final: 0.7722 (tt0) REVERT: B 256 MET cc_start: 0.9052 (tpp) cc_final: 0.8702 (tpp) REVERT: B 422 ARG cc_start: 0.8830 (ttm110) cc_final: 0.8547 (ttm110) REVERT: B 467 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7693 (mp) REVERT: D 24 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: D 126 MET cc_start: 0.8561 (ttt) cc_final: 0.8353 (tpp) REVERT: D 220 ASN cc_start: 0.8578 (m110) cc_final: 0.8342 (m-40) REVERT: E 69 ARG cc_start: 0.9090 (ttt180) cc_final: 0.8555 (ttt180) REVERT: I 1 MET cc_start: 0.8750 (pmm) cc_final: 0.8143 (pmm) REVERT: I 23 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8621 (m-80) REVERT: C 17 GLU cc_start: 0.8355 (pt0) cc_final: 0.8056 (mp0) REVERT: C 72 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8634 (pt0) REVERT: C 456 SER cc_start: 0.7732 (t) cc_final: 0.7516 (m) REVERT: A 37 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7654 (ptm) REVERT: A 64 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7013 (mtm-85) REVERT: A 331 MET cc_start: 0.8516 (mmm) cc_final: 0.8258 (tpt) outliers start: 40 outliers final: 23 residues processed: 177 average time/residue: 1.5417 time to fit residues: 317.1523 Evaluate side-chains 182 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 3.793 ------------------------------------------------------------------------------- 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 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE 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 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 37 MET Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET 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: 5.9990 chunk 6 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 138 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.116929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095968 restraints weight = 29503.877| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.79 r_work: 0.3180 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.229 21061 Z= 0.118 Angle : 0.535 12.487 28997 Z= 0.252 Chirality : 0.039 0.294 2809 Planarity : 0.004 0.059 3572 Dihedral : 14.641 120.196 4054 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % 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: 1.93 (0.19), residues: 2063 helix: 2.49 (0.15), residues: 1257 sheet: -0.19 (0.93), residues: 32 loop : -0.74 (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 C 418 PHE 0.018 0.001 PHE D 113 TYR 0.009 0.001 TYR A 254 ARG 0.009 0.000 ARG B 476 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 986) hydrogen bonds : angle 3.99692 ( 2811) covalent geometry : bond 0.00254 (21032) covalent geometry : angle 0.53524 (28997) Misc. bond : bond 0.04265 ( 29) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.822 Fit side-chains REVERT: B 55 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8474 (ptm) REVERT: B 121 GLU cc_start: 0.7977 (tt0) cc_final: 0.7669 (tt0) REVERT: B 218 CYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8310 (t) REVERT: B 256 MET cc_start: 0.9018 (tpp) cc_final: 0.8666 (tpp) REVERT: B 422 ARG cc_start: 0.8761 (ttm110) cc_final: 0.8528 (ttm110) REVERT: B 467 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7661 (mp) REVERT: D 24 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: D 220 ASN cc_start: 0.8573 (m110) cc_final: 0.8336 (m-40) REVERT: E 38 VAL cc_start: 0.7867 (t) cc_final: 0.7476 (p) REVERT: E 69 ARG cc_start: 0.9077 (ttt180) cc_final: 0.8631 (ttt180) REVERT: I 1 MET cc_start: 0.8705 (pmm) cc_final: 0.8102 (pmm) REVERT: I 23 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8584 (m-80) REVERT: C 17 GLU cc_start: 0.8355 (pt0) cc_final: 0.8055 (mp0) REVERT: C 168 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8006 (mtp) REVERT: C 456 SER cc_start: 0.7708 (t) cc_final: 0.7503 (m) REVERT: A 172 MET cc_start: 0.8975 (ttp) cc_final: 0.8717 (ttt) REVERT: A 331 MET cc_start: 0.8470 (mmm) cc_final: 0.8262 (mmt) outliers start: 32 outliers final: 19 residues processed: 172 average time/residue: 1.2746 time to fit residues: 249.9926 Evaluate side-chains 179 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 170 ASP Chi-restraints excluded: chain B residue 218 CYS 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 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE 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 155 MET Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain 1 residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 114 optimal weight: 0.0370 chunk 186 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.096091 restraints weight = 29523.160| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.79 r_work: 0.3166 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.813 21061 Z= 0.128 Angle : 0.523 9.799 28997 Z= 0.248 Chirality : 0.039 0.289 2809 Planarity : 0.004 0.059 3572 Dihedral : 14.601 120.073 4054 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Rotamer: Outliers : 1.65 % Allowed : 14.76 % Favored : 83.59 % 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: 2.49 (0.15), residues: 1259 sheet: -0.12 (0.94), residues: 32 loop : -0.74 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 21 HIS 0.004 0.001 HIS C 418 PHE 0.018 0.001 PHE D 113 TYR 0.009 0.001 TYR L 35 ARG 0.008 0.000 ARG B 476 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 986) hydrogen bonds : angle 3.97528 ( 2811) covalent geometry : bond 0.00247 (21032) covalent geometry : angle 0.52256 (28997) Misc. bond : bond 0.15099 ( 29) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.866 Fit side-chains REVERT: B 55 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8467 (ptm) REVERT: B 121 GLU cc_start: 0.7982 (tt0) cc_final: 0.7669 (tt0) REVERT: B 218 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8200 (t) REVERT: B 256 MET cc_start: 0.9021 (tpp) cc_final: 0.8662 (tpp) REVERT: B 422 ARG cc_start: 0.8762 (ttm110) cc_final: 0.8524 (ttm110) REVERT: B 467 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7659 (mp) REVERT: D 24 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: D 220 ASN cc_start: 0.8576 (m110) cc_final: 0.8338 (m-40) REVERT: E 38 VAL cc_start: 0.7763 (t) cc_final: 0.7383 (p) REVERT: E 69 ARG cc_start: 0.9065 (ttt180) cc_final: 0.8621 (ttt180) REVERT: I 1 MET cc_start: 0.8705 (pmm) cc_final: 0.7998 (pmm) REVERT: I 23 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: C 17 GLU cc_start: 0.8360 (pt0) cc_final: 0.8044 (mp0) REVERT: C 168 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7984 (mtp) REVERT: C 273 ILE cc_start: 0.8542 (mt) cc_final: 0.8280 (mp) REVERT: C 456 SER cc_start: 0.7688 (t) cc_final: 0.7481 (m) REVERT: A 83 ILE cc_start: 0.8674 (mp) cc_final: 0.8309 (mp) REVERT: A 172 MET cc_start: 0.9027 (ttp) cc_final: 0.8761 (ttt) outliers start: 28 outliers final: 19 residues processed: 169 average time/residue: 1.3369 time to fit residues: 261.3591 Evaluate side-chains 180 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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 170 ASP Chi-restraints excluded: chain B residue 218 CYS 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 B residue 467 ILE 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 289 LEU Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 23 PHE 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 C residue 444 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain 1 residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 192 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 GLN V 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095215 restraints weight = 29827.940| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.81 r_work: 0.3165 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.725 21061 Z= 0.143 Angle : 0.535 10.228 28997 Z= 0.253 Chirality : 0.040 0.290 2809 Planarity : 0.005 0.059 3572 Dihedral : 14.621 120.062 4054 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 1.59 % Allowed : 15.00 % 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: 1.88 (0.19), residues: 2063 helix: 2.42 (0.15), residues: 1265 sheet: -0.17 (0.94), residues: 32 loop : -0.75 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.005 0.001 HIS B 157 PHE 0.023 0.001 PHE D 113 TYR 0.009 0.001 TYR A 126 ARG 0.008 0.000 ARG B 476 Details of bonding type rmsd hydrogen bonds : bond 0.04829 ( 986) hydrogen bonds : angle 3.99815 ( 2811) covalent geometry : bond 0.00305 (21032) covalent geometry : angle 0.53514 (28997) Misc. bond : bond 0.13476 ( 29) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13713.21 seconds wall clock time: 246 minutes 25.52 seconds (14785.52 seconds total)