Starting phenix.real_space_refine on Sun Jun 30 07:27:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/06_2024/8zee_60026_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/06_2024/8zee_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/06_2024/8zee_60026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/06_2024/8zee_60026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/06_2024/8zee_60026_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/06_2024/8zee_60026_neut_updated.pdb" } 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 Residue "B TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A ASP 103": "OD1" <-> "OD2" Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 11.43, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 8.63 Conformation dependent library (CDL) restraints added in 2.9 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... running ksdssp... Secondary structure from input PDB file: 91 helices and 5 sheets defined 60.2% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 9 through 12 Processing helix chain 'B' and resid 16 through 44 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 63 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 93 through 116 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 195 through 218 removed outlier: 4.078A pdb=" N SER B 200 " --> pdb=" O GLY B 197 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA B 205 " --> pdb=" O HIS B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 236 through 258 Processing helix chain 'B' and resid 265 through 268 No H-bonds generated for 'chain 'B' and resid 265 through 268' Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 279 through 295 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'B' and resid 414 through 426 removed outlier: 4.368A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 474 Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 31 through 53 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 101 through 107 Processing helix chain 'D' and resid 109 through 136 Processing helix chain 'D' and resid 141 through 163 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 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 175 through 188 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 195 through 219 Processing helix chain 'D' and resid 246 through 256 Processing helix chain 'D' and resid 264 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 299 through 307 Processing helix chain 'D' and resid 314 through 333 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) Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 349 through 351 No H-bonds generated for 'chain 'D' and resid 349 through 351' Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 17 through 39 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 42 through 47 Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'F' and resid 17 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 25 through 34 Proline residue: H 32 - end of helix Processing helix chain 'H' and resid 47 through 67 Processing helix chain 'H' and resid 81 through 84 Processing helix chain 'I' and resid 2 through 23 Processing helix chain 'K' and resid 13 through 43 Proline residue: K 17 - end of helix Proline residue: K 20 - end of helix Proline residue: K 26 - end of helix Proline residue: K 29 - end of helix removed outlier: 4.071A pdb=" N ILE K 33 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 37 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 5 through 30 Proline residue: M 18 - end of helix Processing helix chain 'T' and resid 2 through 22 Processing helix chain 'V' and resid 3 through 28 removed outlier: 3.946A pdb=" N GLY V 19 " --> pdb=" O VAL V 15 " (cutoff:3.500A) Proline residue: V 20 - end of helix removed outlier: 3.892A pdb=" N VAL V 23 " --> pdb=" O GLY V 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 67 through 97 Processing helix chain 'Z' and resid 2 through 28 Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 37 through 59 Processing helix chain 'C' and resid 16 through 19 No H-bonds generated for 'chain 'C' and resid 16 through 19' Processing helix chain 'C' and resid 23 through 30 removed outlier: 5.885A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 61 Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 77 through 83 removed outlier: 3.866A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 97 through 122 Processing helix chain 'C' and resid 144 through 169 Processing helix chain 'C' and resid 194 through 202 removed outlier: 4.004A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 241 removed outlier: 3.589A pdb=" N TYR C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 256 through 280 Processing helix chain 'C' and resid 287 through 290 No H-bonds generated for 'chain 'C' and resid 287 through 290' Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 341 through 345 removed outlier: 4.015A pdb=" N ARG C 345 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 Proline residue: C 356 - end of helix No H-bonds generated for 'chain 'C' and resid 352 through 357' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 374 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 410 through 441 Processing helix chain 'C' and resid 454 through 456 No H-bonds generated for 'chain 'C' and resid 454 through 456' Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 31 through 54 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 137 removed outlier: 3.581A pdb=" N TRP A 131 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 165 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 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 196 through 222 Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.559A pdb=" N ARG A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 294 removed outlier: 3.626A pdb=" N HIS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 317 through 332 Processing helix chain '1' and resid 45 through 56 Processing helix chain '1' and resid 63 through 77 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= A, first strand: chain 'B' and resid 166 through 169 Processing sheet with id= B, first strand: chain 'B' and resid 343 through 347 Processing sheet with id= C, 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= D, first strand: chain 'B' and resid 369 through 371 Processing sheet with id= E, first strand: chain 'C' and resid 173 through 175 849 hydrogen bonds defined for protein. 2406 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: 5.14 Time building geometry restraints manager: 9.38 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: 84.18 - 102.77: 248 102.77 - 121.35: 22917 121.35 - 139.94: 5723 139.94 - 158.52: 38 158.52 - 177.11: 71 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: 205 2.64 - 3.21: 17813 3.21 - 3.77: 29599 3.77 - 4.34: 41993 4.34 - 4.90: 71286 Nonbonded interactions: 160896 Sorted by model distance: nonbonded pdb=" O ASP D 297 " pdb=" OH TYR D 315 " model vdw 2.080 2.440 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 2.440 nonbonded pdb=" O GLY C 390 " pdb=" ND2 ASN A 298 " model vdw 2.191 2.520 nonbonded pdb=" O ARG B 127 " pdb=" OG1 THR B 128 " model vdw 2.218 2.440 ... (remaining 160891 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.600 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 52.760 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.178 21032 Z= 0.371 Angle : 1.193 18.453 28997 Z= 0.448 Chirality : 0.040 0.221 2809 Planarity : 0.014 0.149 3572 Dihedral : 18.029 135.215 7567 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.67 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.19), residues: 2063 helix: 2.10 (0.15), residues: 1251 sheet: -0.60 (0.80), residues: 42 loop : -0.69 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 113 HIS 0.006 0.001 HIS B 202 PHE 0.051 0.001 PHE D 185 TYR 0.009 0.001 TYR D 296 ARG 0.009 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.759 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: 1.1130 time to fit residues: 223.2144 Evaluate side-chains 141 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.858 ------------------------------------------------------------------------------- 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: 2.9990 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 0.0370 chunk 159 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21032 Z= 0.168 Angle : 0.597 13.475 28997 Z= 0.266 Chirality : 0.042 0.336 2809 Planarity : 0.005 0.058 3572 Dihedral : 16.650 122.329 4058 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 1.65 % Allowed : 6.35 % Favored : 92.00 % 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: 1.67 (0.19), residues: 2063 helix: 2.17 (0.15), residues: 1245 sheet: -0.24 (0.91), residues: 32 loop : -0.59 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 113 HIS 0.007 0.001 HIS C 429 PHE 0.017 0.001 PHE D 113 TYR 0.010 0.001 TYR H 68 ARG 0.007 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.890 Fit side-chains REVERT: B 37 MET cc_start: 0.8333 (mmm) cc_final: 0.8071 (tpt) REVERT: B 256 MET cc_start: 0.8792 (tpp) cc_final: 0.8488 (tpp) REVERT: D 220 ASN cc_start: 0.8280 (m110) cc_final: 0.7985 (m-40) REVERT: I 23 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: C 168 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8099 (mtp) REVERT: A 132 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: A 172 MET cc_start: 0.8632 (ttp) cc_final: 0.8426 (ttt) REVERT: A 331 MET cc_start: 0.8229 (mmm) cc_final: 0.8021 (tpt) outliers start: 28 outliers final: 9 residues processed: 152 average time/residue: 1.1912 time to fit residues: 208.1178 Evaluate side-chains 151 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain F residue 39 MET Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 222 SER 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 102 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** F 40 GLN V 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21032 Z= 0.185 Angle : 0.549 8.792 28997 Z= 0.252 Chirality : 0.040 0.311 2809 Planarity : 0.005 0.057 3572 Dihedral : 15.464 121.079 4054 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 2.00 % Allowed : 9.12 % Favored : 88.88 % 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: 1.66 (0.19), residues: 2063 helix: 2.18 (0.15), residues: 1244 sheet: -0.06 (0.91), residues: 32 loop : -0.64 (0.22), residues: 787 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 0.021 0.001 PHE D 113 TYR 0.010 0.001 TYR E 55 ARG 0.006 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 1.724 Fit side-chains REVERT: B 37 MET cc_start: 0.8330 (mmm) cc_final: 0.7874 (tpt) REVERT: B 256 MET cc_start: 0.8817 (tpp) cc_final: 0.8522 (tpp) REVERT: D 220 ASN cc_start: 0.8305 (m110) cc_final: 0.8016 (m-40) REVERT: E 55 TYR cc_start: 0.8977 (m-80) cc_final: 0.8666 (m-80) REVERT: E 69 ARG cc_start: 0.8890 (ttt180) cc_final: 0.8348 (ttt180) REVERT: I 23 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8556 (m-80) REVERT: C 234 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7994 (mp) REVERT: A 59 ASP cc_start: 0.7595 (p0) cc_final: 0.7391 (p0) REVERT: A 172 MET cc_start: 0.8606 (ttp) cc_final: 0.8401 (ttt) REVERT: A 183 MET cc_start: 0.8829 (mtm) cc_final: 0.8596 (mtp) outliers start: 34 outliers final: 14 residues processed: 164 average time/residue: 1.2177 time to fit residues: 228.8184 Evaluate side-chains 162 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP 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 330 MET Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 80 SER 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 234 LEU Chi-restraints excluded: chain A residue 63 ILE 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 183 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 0.0270 chunk 20 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 124 optimal weight: 0.0470 chunk 186 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21032 Z= 0.140 Angle : 0.518 8.835 28997 Z= 0.237 Chirality : 0.039 0.297 2809 Planarity : 0.004 0.057 3572 Dihedral : 15.035 120.195 4054 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 2.12 % Allowed : 11.12 % Favored : 86.76 % 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: 1.81 (0.19), residues: 2063 helix: 2.29 (0.15), residues: 1245 sheet: 0.09 (0.92), residues: 32 loop : -0.57 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 51 HIS 0.004 0.001 HIS C 418 PHE 0.015 0.001 PHE D 113 TYR 0.008 0.001 TYR A 126 ARG 0.005 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 1.868 Fit side-chains REVERT: B 37 MET cc_start: 0.8324 (mmm) cc_final: 0.8072 (tpt) REVERT: B 81 SER cc_start: 0.8983 (p) cc_final: 0.8633 (m) REVERT: B 256 MET cc_start: 0.8826 (tpp) cc_final: 0.8424 (tpp) REVERT: B 422 ARG cc_start: 0.8492 (ttm110) cc_final: 0.8213 (ttm110) REVERT: D 126 MET cc_start: 0.8367 (ttt) cc_final: 0.8056 (ttt) REVERT: D 220 ASN cc_start: 0.8267 (m110) cc_final: 0.7954 (m-40) REVERT: E 69 ARG cc_start: 0.8875 (ttt180) cc_final: 0.8379 (ttt180) REVERT: I 23 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: A 64 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7155 (mpt180) REVERT: A 172 MET cc_start: 0.8590 (ttp) cc_final: 0.8328 (ttt) outliers start: 36 outliers final: 15 residues processed: 170 average time/residue: 1.1655 time to fit residues: 228.1690 Evaluate side-chains 169 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 255 PHE 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 164 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 81 optimal weight: 0.0870 chunk 168 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 HIS F 23 HIS V 32 ASN C 16 GLN A 322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21032 Z= 0.153 Angle : 0.519 8.550 28997 Z= 0.240 Chirality : 0.039 0.288 2809 Planarity : 0.004 0.057 3572 Dihedral : 14.890 120.076 4054 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 2.24 % Allowed : 11.94 % Favored : 85.82 % 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: 1.82 (0.19), residues: 2063 helix: 2.29 (0.15), residues: 1246 sheet: 0.17 (0.93), residues: 32 loop : -0.56 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.004 0.001 HIS C 418 PHE 0.017 0.001 PHE D 113 TYR 0.008 0.001 TYR A 126 ARG 0.005 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 1.769 Fit side-chains REVERT: B 37 MET cc_start: 0.8327 (mmm) cc_final: 0.8081 (tpt) REVERT: B 81 SER cc_start: 0.9005 (p) cc_final: 0.8676 (m) REVERT: B 256 MET cc_start: 0.8830 (tpp) cc_final: 0.8443 (tpp) REVERT: B 422 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8193 (ttm110) REVERT: D 85 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.7314 (mmm) REVERT: D 220 ASN cc_start: 0.8268 (m110) cc_final: 0.7957 (m-40) REVERT: E 69 ARG cc_start: 0.8885 (ttt180) cc_final: 0.8375 (ttt180) REVERT: I 23 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: A 64 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7219 (mpt180) REVERT: A 172 MET cc_start: 0.8579 (ttp) cc_final: 0.8336 (ttt) REVERT: A 331 MET cc_start: 0.8292 (mmm) cc_final: 0.7957 (tpt) outliers start: 38 outliers final: 20 residues processed: 171 average time/residue: 1.2432 time to fit residues: 243.1097 Evaluate side-chains 174 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain 1 residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 38 optimal weight: 0.0980 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 0.1980 chunk 197 optimal weight: 3.9990 chunk 163 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21032 Z= 0.133 Angle : 0.498 9.167 28997 Z= 0.231 Chirality : 0.038 0.271 2809 Planarity : 0.004 0.057 3572 Dihedral : 14.661 120.081 4054 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Rotamer: Outliers : 1.94 % Allowed : 12.41 % Favored : 85.65 % 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: 1.91 (0.19), residues: 2063 helix: 2.39 (0.15), residues: 1242 sheet: 0.20 (0.93), residues: 32 loop : -0.56 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 51 HIS 0.004 0.001 HIS C 418 PHE 0.015 0.001 PHE D 113 TYR 0.007 0.001 TYR A 254 ARG 0.008 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 1.738 Fit side-chains REVERT: B 37 MET cc_start: 0.8335 (mmm) cc_final: 0.8072 (tpt) REVERT: B 81 SER cc_start: 0.9027 (p) cc_final: 0.8724 (m) REVERT: B 256 MET cc_start: 0.8836 (tpp) cc_final: 0.8459 (tpp) REVERT: B 422 ARG cc_start: 0.8414 (ttm110) cc_final: 0.8159 (ttm110) REVERT: D 85 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.7287 (mmm) REVERT: D 220 ASN cc_start: 0.8263 (m110) cc_final: 0.7949 (m-40) REVERT: I 23 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8490 (m-80) REVERT: A 266 ASN cc_start: 0.7573 (t0) cc_final: 0.7312 (t160) REVERT: A 331 MET cc_start: 0.8269 (mmm) cc_final: 0.8050 (tpt) outliers start: 33 outliers final: 17 residues processed: 169 average time/residue: 1.2706 time to fit residues: 245.8410 Evaluate side-chains 165 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 196 optimal weight: 0.0070 chunk 123 optimal weight: 0.0670 chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 ASN V 32 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21032 Z= 0.146 Angle : 0.505 9.126 28997 Z= 0.236 Chirality : 0.039 0.260 2809 Planarity : 0.004 0.057 3572 Dihedral : 14.576 120.078 4054 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.76 % Allowed : 13.24 % Favored : 85.00 % 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: 1.92 (0.19), residues: 2063 helix: 2.40 (0.15), residues: 1242 sheet: 0.22 (0.93), residues: 32 loop : -0.56 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.004 0.001 HIS C 418 PHE 0.016 0.001 PHE D 113 TYR 0.008 0.001 TYR E 55 ARG 0.008 0.000 ARG C 378 *********************** 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 188 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 1.779 Fit side-chains REVERT: B 37 MET cc_start: 0.8351 (mmm) cc_final: 0.8067 (tpt) REVERT: B 81 SER cc_start: 0.9022 (p) cc_final: 0.8738 (m) REVERT: B 256 MET cc_start: 0.8823 (tpp) cc_final: 0.8457 (tpp) REVERT: B 422 ARG cc_start: 0.8423 (ttm110) cc_final: 0.8153 (ttm110) REVERT: D 220 ASN cc_start: 0.8257 (m110) cc_final: 0.7933 (m-40) REVERT: I 23 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8564 (m-80) REVERT: A 64 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7408 (mpt180) REVERT: A 266 ASN cc_start: 0.7700 (t0) cc_final: 0.7402 (t160) REVERT: A 331 MET cc_start: 0.8273 (mmm) cc_final: 0.8059 (tpt) outliers start: 30 outliers final: 20 residues processed: 170 average time/residue: 1.2364 time to fit residues: 240.5349 Evaluate side-chains 172 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain 1 residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 178 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21032 Z= 0.166 Angle : 0.518 12.350 28997 Z= 0.242 Chirality : 0.039 0.252 2809 Planarity : 0.004 0.056 3572 Dihedral : 14.533 120.314 4054 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.88 % Allowed : 13.24 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.36 (0.15), residues: 1243 sheet: 0.29 (0.93), residues: 32 loop : -0.57 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.004 0.001 HIS C 429 PHE 0.016 0.001 PHE B 246 TYR 0.009 0.001 TYR D 296 ARG 0.008 0.000 ARG C 378 *********************** 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 191 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 2.037 Fit side-chains REVERT: B 37 MET cc_start: 0.8402 (mmm) cc_final: 0.8137 (tpt) REVERT: B 81 SER cc_start: 0.9048 (p) cc_final: 0.8796 (m) REVERT: B 256 MET cc_start: 0.8835 (tpp) cc_final: 0.8487 (tpp) REVERT: D 24 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: D 220 ASN cc_start: 0.8268 (m110) cc_final: 0.7971 (m-40) REVERT: I 23 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8604 (m-80) REVERT: A 266 ASN cc_start: 0.7729 (t0) cc_final: 0.7432 (t160) REVERT: A 331 MET cc_start: 0.8298 (mmm) cc_final: 0.8092 (tpt) outliers start: 32 outliers final: 22 residues processed: 173 average time/residue: 1.1623 time to fit residues: 231.9607 Evaluate side-chains 175 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 329 MET Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain 1 residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 32 ASN A 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21032 Z= 0.175 Angle : 0.534 13.443 28997 Z= 0.248 Chirality : 0.039 0.238 2809 Planarity : 0.004 0.056 3572 Dihedral : 14.495 120.396 4054 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.71 % Allowed : 13.76 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 2063 helix: 2.31 (0.15), residues: 1249 sheet: 0.49 (0.95), residues: 32 loop : -0.60 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.005 0.001 HIS B 157 PHE 0.018 0.001 PHE D 113 TYR 0.010 0.001 TYR A 126 ARG 0.009 0.000 ARG C 378 *********************** 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 189 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.828 Fit side-chains REVERT: B 37 MET cc_start: 0.8390 (mmm) cc_final: 0.8066 (tpt) REVERT: B 256 MET cc_start: 0.8844 (tpp) cc_final: 0.8483 (tpp) REVERT: D 24 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: D 220 ASN cc_start: 0.8317 (m110) cc_final: 0.8001 (m-40) REVERT: I 23 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8616 (m-80) REVERT: I 25 SER cc_start: 0.8637 (t) cc_final: 0.8433 (p) REVERT: A 266 ASN cc_start: 0.7643 (t0) cc_final: 0.7328 (t160) REVERT: A 331 MET cc_start: 0.8300 (mmm) cc_final: 0.8091 (tpt) outliers start: 29 outliers final: 24 residues processed: 173 average time/residue: 1.1159 time to fit residues: 223.1554 Evaluate side-chains 180 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 329 MET Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain 1 residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 10.0000 chunk 118 optimal weight: 0.1980 chunk 91 optimal weight: 0.4980 chunk 134 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 99 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21032 Z= 0.145 Angle : 0.518 18.715 28997 Z= 0.241 Chirality : 0.038 0.219 2809 Planarity : 0.004 0.056 3572 Dihedral : 14.238 120.174 4054 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.35 % Allowed : 14.82 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.36 (0.15), residues: 1248 sheet: 0.41 (0.94), residues: 32 loop : -0.59 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.004 0.001 HIS C 418 PHE 0.016 0.001 PHE D 113 TYR 0.008 0.001 TYR A 126 ARG 0.009 0.000 ARG C 378 ********************** 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 182 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 1.474 Fit side-chains REVERT: B 37 MET cc_start: 0.8403 (mmm) cc_final: 0.8133 (tpt) REVERT: B 256 MET cc_start: 0.8836 (tpp) cc_final: 0.8484 (tpp) REVERT: D 24 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: D 220 ASN cc_start: 0.8301 (m110) cc_final: 0.7976 (m-40) REVERT: F 40 GLN cc_start: 0.8592 (tp40) cc_final: 0.8381 (mm110) REVERT: I 23 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8536 (m-80) REVERT: C 273 ILE cc_start: 0.8327 (mt) cc_final: 0.8057 (mp) REVERT: A 266 ASN cc_start: 0.7621 (t0) cc_final: 0.7312 (t160) REVERT: A 331 MET cc_start: 0.8293 (mmm) cc_final: 0.8039 (tpt) outliers start: 23 outliers final: 17 residues processed: 169 average time/residue: 1.1440 time to fit residues: 223.1860 Evaluate side-chains 172 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 329 MET Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain 1 residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0170 chunk 49 optimal weight: 0.2980 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 331 ASN V 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.097921 restraints weight = 29548.314| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.79 r_work: 0.3197 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21032 Z= 0.141 Angle : 0.496 9.388 28997 Z= 0.235 Chirality : 0.038 0.219 2809 Planarity : 0.004 0.056 3572 Dihedral : 14.096 119.892 4054 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.65 % Allowed : 14.82 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.19), residues: 2063 helix: 2.41 (0.15), residues: 1248 sheet: 0.54 (0.95), residues: 32 loop : -0.58 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 247 HIS 0.004 0.001 HIS C 418 PHE 0.016 0.001 PHE D 113 TYR 0.008 0.001 TYR E 55 ARG 0.009 0.000 ARG B 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5097.92 seconds wall clock time: 90 minutes 54.27 seconds (5454.27 seconds total)