Starting phenix.real_space_refine on Fri Mar 15 00:41:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f24_31427/03_2024/7f24_31427_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f24_31427/03_2024/7f24_31427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f24_31427/03_2024/7f24_31427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f24_31427/03_2024/7f24_31427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f24_31427/03_2024/7f24_31427_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f24_31427/03_2024/7f24_31427_updated.pdb" } resolution = 4.16 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3054 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 47 5.16 5 C 4549 2.51 5 N 1251 2.21 5 O 1315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 50": "NH1" <-> "NH2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 130": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "F ARG 226": "NH1" <-> "NH2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F ARG 266": "NH1" <-> "NH2" Residue "F PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "D GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7165 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1860 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2208 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 9, 'TRANS': 267} Chain breaks: 3 Chain: "B" Number of atoms: 2629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 2605 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 341, 2605 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2624 Chain: "D" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 425 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP B 27 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP B 27 " occ=0.55 Time building chain proxies: 4.80, per 1000 atoms: 0.67 Number of scatterers: 7165 At special positions: 0 Unit cell: (79.351, 94.569, 115.222, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 3 15.00 O 1315 8.00 N 1251 7.00 C 4549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.02 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=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.6 seconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 8 sheets defined 45.0% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 20 through 39 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.633A pdb=" N CYS A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N PHE A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 238' Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.942A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 391 Processing helix chain 'F' and resid 21 through 50 Processing helix chain 'F' and resid 59 through 87 removed outlier: 3.611A pdb=" N VAL F 63 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Proline residue: F 79 - end of helix Processing helix chain 'F' and resid 93 through 126 removed outlier: 4.090A pdb=" N ASN F 97 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER F 107 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER F 110 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 111 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER F 126 " --> pdb=" O TRP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 134 Processing helix chain 'F' and resid 137 through 160 Proline residue: F 158 - end of helix Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 204 through 236 Processing helix chain 'F' and resid 265 through 297 Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 310 through 331 removed outlier: 3.659A pdb=" N SER F 324 " --> pdb=" O GLY F 320 " (cutoff:3.500A) Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 335 through 345 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.239A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.278A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.747A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.974A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.639A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.699A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.581A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.675A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.659A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2321 1.34 - 1.46: 1562 1.46 - 1.58: 3366 1.58 - 1.69: 5 1.69 - 1.81: 64 Bond restraints: 7318 Sorted by residual: bond pdb=" CA SER F 110 " pdb=" C SER F 110 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.24e-02 6.50e+03 5.37e+00 bond pdb=" CB TRP F 148 " pdb=" CG TRP F 148 " ideal model delta sigma weight residual 1.498 1.427 0.071 3.10e-02 1.04e+03 5.20e+00 bond pdb=" CA ASN A 371 " pdb=" C ASN A 371 " ideal model delta sigma weight residual 1.518 1.429 0.089 4.01e-02 6.22e+02 4.97e+00 bond pdb=" CB TRP F 318 " pdb=" CG TRP F 318 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.51e+00 bond pdb=" CB PHE F 62 " pdb=" CG PHE F 62 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.25e+00 ... (remaining 7313 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.61: 100 105.61 - 112.74: 3950 112.74 - 119.87: 2646 119.87 - 127.00: 3146 127.00 - 134.14: 87 Bond angle restraints: 9929 Sorted by residual: angle pdb=" C PHE A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta sigma weight residual 121.18 128.28 -7.10 1.98e+00 2.55e-01 1.28e+01 angle pdb=" C PHE A 222 " pdb=" CA PHE A 222 " pdb=" CB PHE A 222 " ideal model delta sigma weight residual 109.70 103.24 6.46 1.81e+00 3.05e-01 1.27e+01 angle pdb=" N HIS A 41 " pdb=" CA HIS A 41 " pdb=" C HIS A 41 " ideal model delta sigma weight residual 108.41 114.07 -5.66 1.61e+00 3.86e-01 1.24e+01 angle pdb=" C LYS A 211 " pdb=" N PHE A 212 " pdb=" CA PHE A 212 " ideal model delta sigma weight residual 122.29 116.69 5.60 1.65e+00 3.67e-01 1.15e+01 angle pdb=" N GLY B 131 " pdb=" CA GLY B 131 " pdb=" C GLY B 131 " ideal model delta sigma weight residual 113.18 121.12 -7.94 2.37e+00 1.78e-01 1.12e+01 ... (remaining 9924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 4253 34.37 - 68.74: 85 68.74 - 103.11: 8 103.11 - 137.48: 1 137.48 - 171.85: 2 Dihedral angle restraints: 4349 sinusoidal: 1707 harmonic: 2642 Sorted by residual: dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -118.88 -171.85 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -50.08 154.67 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual -56.21 56.51 -112.72 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 4346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 613 0.039 - 0.078: 336 0.078 - 0.117: 128 0.117 - 0.155: 38 0.155 - 0.194: 10 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CB ILE F 308 " pdb=" CA ILE F 308 " pdb=" CG1 ILE F 308 " pdb=" CG2 ILE F 308 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CA HIS B 311 " pdb=" N HIS B 311 " pdb=" C HIS B 311 " pdb=" CB HIS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 1122 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 109 " -0.040 2.00e-02 2.50e+03 7.93e-02 6.28e+01 pdb=" C ALA F 109 " 0.137 2.00e-02 2.50e+03 pdb=" O ALA F 109 " -0.051 2.00e-02 2.50e+03 pdb=" N SER F 110 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 327 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.26e+00 pdb=" N PRO A 328 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 328 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 328 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 338 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C LYS A 338 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS A 338 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR A 339 " -0.015 2.00e-02 2.50e+03 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 194 2.64 - 3.21: 7524 3.21 - 3.77: 11828 3.77 - 4.34: 15949 4.34 - 4.90: 25220 Nonbonded interactions: 60715 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.076 2.440 nonbonded pdb=" OG BSER B 227 " pdb=" OG SER B 245 " model vdw 2.168 2.440 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.174 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.176 2.440 nonbonded pdb=" OG ASER B 227 " pdb=" OG SER B 245 " model vdw 2.178 2.440 ... (remaining 60710 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 1.690 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 24.520 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.009 0.089 7318 Z= 0.580 Angle : 1.045 10.612 9929 Z= 0.611 Chirality : 0.056 0.194 1125 Planarity : 0.007 0.079 1256 Dihedral : 15.531 171.855 2628 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 0.65 % Allowed : 10.64 % Favored : 88.72 % 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: -2.40 (0.24), residues: 890 helix: -1.64 (0.21), residues: 409 sheet: -0.83 (0.36), residues: 184 loop : -1.68 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 318 HIS 0.015 0.003 HIS A 357 PHE 0.040 0.003 PHE A 238 TYR 0.018 0.003 TYR F 218 ARG 0.006 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 212 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7824 (mttp) cc_final: 0.7483 (tttt) REVERT: A 360 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: F 105 MET cc_start: 0.9125 (ttp) cc_final: 0.8647 (tmm) REVERT: F 289 PHE cc_start: 0.8119 (m-80) cc_final: 0.7681 (m-80) REVERT: F 333 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8036 (p90) REVERT: B 6 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7587 (mm-40) REVERT: B 52 ARG cc_start: 0.7499 (mtt-85) cc_final: 0.7286 (mtt90) REVERT: B 61 MET cc_start: 0.8636 (ppp) cc_final: 0.8178 (ppp) REVERT: B 70 LEU cc_start: 0.7371 (pt) cc_final: 0.7037 (mp) REVERT: B 78 LYS cc_start: 0.6658 (mmmt) cc_final: 0.6117 (tppt) REVERT: B 85 TYR cc_start: 0.8582 (m-10) cc_final: 0.8369 (m-80) REVERT: B 209 LYS cc_start: 0.7814 (mttp) cc_final: 0.7560 (mttp) REVERT: B 295 ASN cc_start: 0.6510 (m110) cc_final: 0.6124 (t0) REVERT: B 297 TRP cc_start: 0.6352 (m100) cc_final: 0.5755 (m100) REVERT: B 335 PHE cc_start: 0.7217 (m-80) cc_final: 0.6521 (m-80) REVERT: D 32 LYS cc_start: 0.8578 (tptp) cc_final: 0.8333 (tptt) outliers start: 3 outliers final: 0 residues processed: 214 average time/residue: 0.1962 time to fit residues: 54.9467 Evaluate side-chains 163 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN B 36 ASN B 62 HIS ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7318 Z= 0.192 Angle : 0.614 7.536 9929 Z= 0.327 Chirality : 0.045 0.219 1125 Planarity : 0.005 0.050 1256 Dihedral : 9.468 166.726 1003 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.39 % Allowed : 2.98 % Favored : 96.63 % 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: -0.58 (0.26), residues: 890 helix: 0.06 (0.24), residues: 405 sheet: -0.08 (0.42), residues: 135 loop : -0.89 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.007 0.001 HIS A 220 PHE 0.022 0.002 PHE F 333 TYR 0.021 0.002 TYR B 59 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7741 (mttp) cc_final: 0.7359 (tttt) REVERT: A 277 TRP cc_start: 0.8605 (t-100) cc_final: 0.8201 (t-100) REVERT: A 378 ASP cc_start: 0.9138 (m-30) cc_final: 0.8859 (m-30) REVERT: A 386 MET cc_start: 0.8005 (tmm) cc_final: 0.7604 (tpp) REVERT: F 35 LEU cc_start: 0.9152 (mt) cc_final: 0.8938 (mt) REVERT: F 70 ASP cc_start: 0.8557 (m-30) cc_final: 0.8274 (m-30) REVERT: F 105 MET cc_start: 0.8800 (ttp) cc_final: 0.8419 (tmm) REVERT: F 222 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: F 289 PHE cc_start: 0.7918 (m-80) cc_final: 0.7495 (m-80) REVERT: F 324 SER cc_start: 0.8674 (m) cc_final: 0.8134 (m) REVERT: F 327 ASN cc_start: 0.8568 (m110) cc_final: 0.7852 (m110) REVERT: F 337 PHE cc_start: 0.7873 (m-80) cc_final: 0.7649 (m-80) REVERT: B 61 MET cc_start: 0.8462 (ppp) cc_final: 0.8154 (ppp) REVERT: B 85 TYR cc_start: 0.8711 (m-10) cc_final: 0.8185 (m-80) REVERT: B 110 ASN cc_start: 0.7739 (t0) cc_final: 0.7533 (t0) REVERT: B 172 GLU cc_start: 0.8385 (tp30) cc_final: 0.7959 (tm-30) REVERT: B 228 ASP cc_start: 0.8101 (m-30) cc_final: 0.7494 (m-30) REVERT: B 295 ASN cc_start: 0.6376 (m110) cc_final: 0.6134 (t0) REVERT: B 297 TRP cc_start: 0.6069 (m100) cc_final: 0.5639 (m100) REVERT: B 313 ASN cc_start: 0.6589 (t0) cc_final: 0.6023 (m-40) REVERT: B 335 PHE cc_start: 0.7215 (m-80) cc_final: 0.6742 (m-80) REVERT: D 32 LYS cc_start: 0.8718 (tptp) cc_final: 0.8321 (tptt) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.1850 time to fit residues: 60.9245 Evaluate side-chains 188 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 40.0000 chunk 71 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 7318 Z= 0.346 Angle : 0.690 7.695 9929 Z= 0.366 Chirality : 0.046 0.187 1125 Planarity : 0.005 0.045 1256 Dihedral : 9.566 164.185 1003 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.39 % Allowed : 4.80 % Favored : 94.81 % 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: -0.46 (0.27), residues: 890 helix: 0.34 (0.24), residues: 398 sheet: -0.32 (0.41), residues: 147 loop : -0.93 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 99 HIS 0.018 0.002 HIS A 220 PHE 0.026 0.003 PHE F 333 TYR 0.021 0.002 TYR A 360 ARG 0.004 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7665 (mttp) cc_final: 0.7368 (tttt) REVERT: A 235 ILE cc_start: 0.7949 (mm) cc_final: 0.7574 (mm) REVERT: A 386 MET cc_start: 0.8112 (tmm) cc_final: 0.7738 (tpp) REVERT: A 390 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8010 (tm-30) REVERT: F 92 PHE cc_start: 0.6359 (m-80) cc_final: 0.6058 (m-10) REVERT: F 105 MET cc_start: 0.8965 (ttp) cc_final: 0.8724 (ttp) REVERT: F 289 PHE cc_start: 0.7997 (m-80) cc_final: 0.7532 (m-80) REVERT: F 321 TRP cc_start: 0.9237 (m-10) cc_final: 0.8996 (m-10) REVERT: F 324 SER cc_start: 0.8760 (m) cc_final: 0.8211 (m) REVERT: F 327 ASN cc_start: 0.8593 (m110) cc_final: 0.8200 (m110) REVERT: B 85 TYR cc_start: 0.8567 (m-10) cc_final: 0.8281 (m-80) REVERT: B 124 TYR cc_start: 0.7980 (m-10) cc_final: 0.7656 (m-10) REVERT: B 138 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 172 GLU cc_start: 0.8399 (tp30) cc_final: 0.7887 (tm-30) REVERT: B 212 ASP cc_start: 0.7161 (t0) cc_final: 0.6934 (t0) REVERT: B 220 GLN cc_start: 0.8140 (pp30) cc_final: 0.7879 (pp30) REVERT: B 228 ASP cc_start: 0.8264 (m-30) cc_final: 0.7725 (m-30) REVERT: B 280 LYS cc_start: 0.6073 (ttpt) cc_final: 0.5671 (ttpp) REVERT: B 297 TRP cc_start: 0.5766 (m100) cc_final: 0.5464 (m100) REVERT: D 32 LYS cc_start: 0.8658 (tptp) cc_final: 0.8303 (tptt) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1645 time to fit residues: 46.5081 Evaluate side-chains 162 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7318 Z= 0.236 Angle : 0.619 8.999 9929 Z= 0.325 Chirality : 0.044 0.193 1125 Planarity : 0.004 0.048 1256 Dihedral : 9.396 161.195 1003 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.26 % Allowed : 2.85 % Favored : 96.89 % 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: -0.10 (0.27), residues: 890 helix: 0.68 (0.25), residues: 397 sheet: -0.09 (0.40), residues: 151 loop : -0.83 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 99 HIS 0.006 0.001 HIS A 220 PHE 0.021 0.002 PHE F 333 TYR 0.011 0.002 TYR B 289 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8527 (mtmt) cc_final: 0.7829 (mmtt) REVERT: A 34 LYS cc_start: 0.7924 (mttp) cc_final: 0.7618 (tttt) REVERT: A 386 MET cc_start: 0.8110 (tmm) cc_final: 0.7687 (tpp) REVERT: F 70 ASP cc_start: 0.8765 (m-30) cc_final: 0.8512 (m-30) REVERT: F 105 MET cc_start: 0.8873 (ttp) cc_final: 0.8611 (ttp) REVERT: F 289 PHE cc_start: 0.7943 (m-80) cc_final: 0.7525 (m-80) REVERT: F 327 ASN cc_start: 0.8600 (m110) cc_final: 0.8082 (m110) REVERT: B 85 TYR cc_start: 0.8625 (m-10) cc_final: 0.8190 (m-80) REVERT: B 124 TYR cc_start: 0.7853 (m-10) cc_final: 0.7544 (m-10) REVERT: B 172 GLU cc_start: 0.8313 (tp30) cc_final: 0.7843 (tm-30) REVERT: B 220 GLN cc_start: 0.8155 (pp30) cc_final: 0.7865 (pp30) REVERT: B 228 ASP cc_start: 0.8258 (m-30) cc_final: 0.7717 (m-30) REVERT: B 339 TRP cc_start: 0.5407 (m100) cc_final: 0.4851 (m100) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2014 time to fit residues: 55.1304 Evaluate side-chains 166 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 35 optimal weight: 0.0870 chunk 72 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN F 53 HIS ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7318 Z= 0.188 Angle : 0.586 9.369 9929 Z= 0.307 Chirality : 0.044 0.171 1125 Planarity : 0.004 0.049 1256 Dihedral : 9.200 158.024 1003 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.52 % Allowed : 2.46 % Favored : 97.02 % 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: 0.01 (0.28), residues: 890 helix: 0.83 (0.25), residues: 403 sheet: -0.31 (0.39), residues: 155 loop : -0.73 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 99 HIS 0.006 0.001 HIS A 220 PHE 0.022 0.002 PHE A 222 TYR 0.016 0.001 TYR A 37 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8492 (mtmt) cc_final: 0.7893 (mmtt) REVERT: A 34 LYS cc_start: 0.7886 (mttp) cc_final: 0.7584 (tttt) REVERT: A 291 LEU cc_start: 0.9170 (mt) cc_final: 0.8803 (mt) REVERT: A 360 TYR cc_start: 0.8718 (m-80) cc_final: 0.8488 (m-80) REVERT: F 105 MET cc_start: 0.8891 (ttp) cc_final: 0.8629 (ttp) REVERT: F 222 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: F 289 PHE cc_start: 0.7933 (m-80) cc_final: 0.7632 (m-80) REVERT: F 324 SER cc_start: 0.8641 (m) cc_final: 0.7946 (m) REVERT: F 327 ASN cc_start: 0.8618 (m110) cc_final: 0.8077 (m110) REVERT: B 65 THR cc_start: 0.7360 (p) cc_final: 0.7145 (p) REVERT: B 85 TYR cc_start: 0.8531 (m-10) cc_final: 0.8159 (m-80) REVERT: B 124 TYR cc_start: 0.7804 (m-10) cc_final: 0.7436 (m-10) REVERT: B 172 GLU cc_start: 0.8301 (tp30) cc_final: 0.7842 (tm-30) REVERT: B 228 ASP cc_start: 0.8269 (m-30) cc_final: 0.7714 (m-30) REVERT: B 284 LEU cc_start: 0.8059 (tp) cc_final: 0.7834 (tp) outliers start: 2 outliers final: 1 residues processed: 208 average time/residue: 0.1657 time to fit residues: 47.4759 Evaluate side-chains 168 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN F 53 HIS ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7318 Z= 0.158 Angle : 0.580 10.686 9929 Z= 0.303 Chirality : 0.044 0.192 1125 Planarity : 0.004 0.051 1256 Dihedral : 9.107 154.309 1003 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.26 % Allowed : 2.33 % Favored : 97.41 % 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: 0.09 (0.28), residues: 890 helix: 0.92 (0.25), residues: 407 sheet: -0.30 (0.39), residues: 155 loop : -0.74 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 99 HIS 0.005 0.001 HIS A 220 PHE 0.032 0.002 PHE A 238 TYR 0.013 0.001 TYR A 37 ARG 0.002 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8509 (mtmt) cc_final: 0.7902 (mmtt) REVERT: A 345 PHE cc_start: 0.8303 (m-80) cc_final: 0.7964 (m-80) REVERT: A 360 TYR cc_start: 0.8566 (m-80) cc_final: 0.7720 (m-80) REVERT: F 138 LYS cc_start: 0.8800 (tttt) cc_final: 0.8425 (tttt) REVERT: F 289 PHE cc_start: 0.7939 (m-80) cc_final: 0.7724 (m-80) REVERT: F 323 ASN cc_start: 0.9243 (t0) cc_final: 0.8882 (t0) REVERT: F 324 SER cc_start: 0.8726 (m) cc_final: 0.8158 (m) REVERT: F 327 ASN cc_start: 0.8693 (m110) cc_final: 0.7826 (m110) REVERT: B 58 ILE cc_start: 0.8286 (tp) cc_final: 0.8083 (tp) REVERT: B 65 THR cc_start: 0.7422 (p) cc_final: 0.7201 (p) REVERT: B 85 TYR cc_start: 0.8477 (m-10) cc_final: 0.8048 (m-80) REVERT: B 105 TYR cc_start: 0.6925 (t80) cc_final: 0.6558 (t80) REVERT: B 124 TYR cc_start: 0.7762 (m-10) cc_final: 0.7493 (m-10) REVERT: B 172 GLU cc_start: 0.8296 (tp30) cc_final: 0.7871 (tm-30) REVERT: B 220 GLN cc_start: 0.8313 (pp30) cc_final: 0.7986 (pp30) REVERT: B 228 ASP cc_start: 0.8147 (m-30) cc_final: 0.7669 (m-30) REVERT: B 284 LEU cc_start: 0.7887 (tp) cc_final: 0.7672 (tp) REVERT: B 313 ASN cc_start: 0.6331 (t0) cc_final: 0.5629 (m-40) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1487 time to fit residues: 47.6617 Evaluate side-chains 180 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 9.9990 chunk 48 optimal weight: 0.0670 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 33 optimal weight: 0.0030 overall best weight: 1.9732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 271 ASN F 53 HIS ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7318 Z= 0.214 Angle : 0.605 9.148 9929 Z= 0.314 Chirality : 0.044 0.183 1125 Planarity : 0.004 0.050 1256 Dihedral : 9.014 152.759 1003 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.26 % Allowed : 1.30 % Favored : 98.44 % 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: 0.04 (0.27), residues: 890 helix: 0.88 (0.25), residues: 397 sheet: -0.34 (0.40), residues: 155 loop : -0.70 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 297 HIS 0.009 0.001 HIS B 54 PHE 0.021 0.002 PHE A 340 TYR 0.016 0.001 TYR A 37 ARG 0.002 0.000 ARG F 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8501 (mtmt) cc_final: 0.7924 (mmtt) REVERT: F 78 MET cc_start: 0.8618 (mpp) cc_final: 0.8275 (mtm) REVERT: F 105 MET cc_start: 0.8881 (ttp) cc_final: 0.8630 (ttp) REVERT: F 289 PHE cc_start: 0.7950 (m-80) cc_final: 0.7712 (m-80) REVERT: F 337 PHE cc_start: 0.7344 (m-80) cc_final: 0.7061 (m-80) REVERT: B 65 THR cc_start: 0.7455 (p) cc_final: 0.7225 (p) REVERT: B 85 TYR cc_start: 0.8462 (m-10) cc_final: 0.8078 (m-80) REVERT: B 172 GLU cc_start: 0.8229 (tp30) cc_final: 0.7786 (tm-30) REVERT: B 228 ASP cc_start: 0.8215 (m-30) cc_final: 0.7741 (m-30) REVERT: B 284 LEU cc_start: 0.7946 (tp) cc_final: 0.7728 (tp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1492 time to fit residues: 44.1769 Evaluate side-chains 164 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 0.0270 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 7318 Z= 0.326 Angle : 0.660 7.990 9929 Z= 0.347 Chirality : 0.046 0.167 1125 Planarity : 0.005 0.049 1256 Dihedral : 9.252 155.603 1003 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.26 % Allowed : 1.17 % Favored : 98.57 % 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: -0.17 (0.27), residues: 890 helix: 0.62 (0.25), residues: 401 sheet: -0.62 (0.39), residues: 161 loop : -0.59 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 297 HIS 0.008 0.002 HIS A 220 PHE 0.021 0.002 PHE A 340 TYR 0.031 0.002 TYR A 37 ARG 0.004 0.000 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8533 (mtmt) cc_final: 0.7814 (tptt) REVERT: A 37 TYR cc_start: 0.8086 (t80) cc_final: 0.7807 (t80) REVERT: A 238 PHE cc_start: 0.6552 (m-80) cc_final: 0.6108 (m-80) REVERT: A 282 LEU cc_start: 0.8934 (mt) cc_final: 0.8488 (mt) REVERT: F 105 MET cc_start: 0.8921 (ttp) cc_final: 0.8592 (ttp) REVERT: F 289 PHE cc_start: 0.7969 (m-80) cc_final: 0.7716 (m-80) REVERT: B 65 THR cc_start: 0.7360 (p) cc_final: 0.7090 (p) REVERT: B 85 TYR cc_start: 0.8472 (m-10) cc_final: 0.8121 (m-80) REVERT: B 99 TRP cc_start: 0.6797 (m-90) cc_final: 0.6290 (m-90) REVERT: B 124 TYR cc_start: 0.8027 (m-10) cc_final: 0.7429 (m-10) REVERT: B 172 GLU cc_start: 0.8279 (tp30) cc_final: 0.7842 (tm-30) REVERT: B 228 ASP cc_start: 0.8267 (m-30) cc_final: 0.7770 (m-30) REVERT: D 36 ASP cc_start: 0.8978 (p0) cc_final: 0.8753 (p0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1577 time to fit residues: 42.9509 Evaluate side-chains 159 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 HIS ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7318 Z= 0.212 Angle : 0.611 11.040 9929 Z= 0.319 Chirality : 0.045 0.175 1125 Planarity : 0.005 0.074 1256 Dihedral : 9.143 154.213 1003 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.26 % Allowed : 0.91 % Favored : 98.83 % 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: -0.12 (0.27), residues: 890 helix: 0.72 (0.25), residues: 406 sheet: -0.52 (0.39), residues: 156 loop : -0.72 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 321 HIS 0.006 0.001 HIS A 220 PHE 0.024 0.002 PHE A 340 TYR 0.027 0.002 TYR A 37 ARG 0.002 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8541 (mtmt) cc_final: 0.7850 (tptt) REVERT: A 37 TYR cc_start: 0.8086 (t80) cc_final: 0.7817 (t80) REVERT: A 360 TYR cc_start: 0.8565 (m-80) cc_final: 0.8229 (m-80) REVERT: F 78 MET cc_start: 0.8880 (mpp) cc_final: 0.8145 (mtm) REVERT: F 289 PHE cc_start: 0.7952 (m-80) cc_final: 0.7732 (m-80) REVERT: F 324 SER cc_start: 0.8762 (m) cc_final: 0.8496 (m) REVERT: B 65 THR cc_start: 0.7344 (p) cc_final: 0.7066 (p) REVERT: B 85 TYR cc_start: 0.8490 (m-10) cc_final: 0.8197 (m-80) REVERT: B 99 TRP cc_start: 0.6870 (m-90) cc_final: 0.6468 (m-90) REVERT: B 110 ASN cc_start: 0.7390 (t0) cc_final: 0.6908 (t0) REVERT: B 124 TYR cc_start: 0.8096 (m-10) cc_final: 0.7631 (m-10) REVERT: B 172 GLU cc_start: 0.8247 (tp30) cc_final: 0.7827 (tm-30) REVERT: B 228 ASP cc_start: 0.8169 (m-30) cc_final: 0.7693 (m-30) REVERT: B 284 LEU cc_start: 0.8027 (tp) cc_final: 0.7799 (tp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1557 time to fit residues: 45.3112 Evaluate side-chains 166 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 HIS ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7318 Z= 0.181 Angle : 0.611 11.485 9929 Z= 0.317 Chirality : 0.045 0.159 1125 Planarity : 0.004 0.058 1256 Dihedral : 8.961 152.580 1003 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.26 % Allowed : 0.39 % Favored : 99.35 % 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: -0.01 (0.27), residues: 890 helix: 0.94 (0.25), residues: 409 sheet: -0.59 (0.39), residues: 155 loop : -0.81 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.017 0.002 HIS D 44 PHE 0.025 0.002 PHE A 340 TYR 0.025 0.001 TYR A 37 ARG 0.001 0.000 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8465 (mtmt) cc_final: 0.7834 (tptt) REVERT: A 37 TYR cc_start: 0.8101 (t80) cc_final: 0.7814 (t80) REVERT: A 282 LEU cc_start: 0.8888 (mt) cc_final: 0.8427 (mt) REVERT: A 345 PHE cc_start: 0.8415 (m-80) cc_final: 0.8080 (m-80) REVERT: A 360 TYR cc_start: 0.8468 (m-80) cc_final: 0.8170 (m-80) REVERT: F 78 MET cc_start: 0.8758 (mpp) cc_final: 0.7996 (mtm) REVERT: F 118 SER cc_start: 0.8323 (m) cc_final: 0.7991 (m) REVERT: F 289 PHE cc_start: 0.7935 (m-80) cc_final: 0.7734 (m-80) REVERT: F 324 SER cc_start: 0.8742 (m) cc_final: 0.8478 (m) REVERT: B 65 THR cc_start: 0.7388 (p) cc_final: 0.7153 (p) REVERT: B 85 TYR cc_start: 0.8523 (m-10) cc_final: 0.8181 (m-80) REVERT: B 99 TRP cc_start: 0.6704 (m-90) cc_final: 0.6386 (m-90) REVERT: B 110 ASN cc_start: 0.7177 (t0) cc_final: 0.6740 (t0) REVERT: B 124 TYR cc_start: 0.7952 (m-10) cc_final: 0.7548 (m-10) REVERT: B 172 GLU cc_start: 0.8207 (tp30) cc_final: 0.7814 (tm-30) REVERT: B 228 ASP cc_start: 0.8113 (m-30) cc_final: 0.7672 (m-30) REVERT: B 284 LEU cc_start: 0.8099 (tp) cc_final: 0.7832 (tp) REVERT: B 325 MET cc_start: 0.8475 (ttp) cc_final: 0.7647 (tpt) REVERT: D 32 LYS cc_start: 0.8719 (tptt) cc_final: 0.8506 (tptt) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1498 time to fit residues: 44.7590 Evaluate side-chains 169 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 HIS ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.128365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.098570 restraints weight = 46327.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.101465 restraints weight = 31505.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.101386 restraints weight = 20660.379| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7318 Z= 0.219 Angle : 0.623 10.807 9929 Z= 0.325 Chirality : 0.044 0.167 1125 Planarity : 0.004 0.051 1256 Dihedral : 8.979 153.306 1003 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.39 % Allowed : 0.26 % Favored : 99.35 % 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: -0.05 (0.27), residues: 890 helix: 0.88 (0.25), residues: 408 sheet: -0.70 (0.39), residues: 161 loop : -0.72 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.013 0.002 HIS D 44 PHE 0.024 0.002 PHE A 340 TYR 0.025 0.002 TYR A 37 ARG 0.002 0.000 ARG F 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1686.47 seconds wall clock time: 31 minutes 21.01 seconds (1881.01 seconds total)