Starting phenix.real_space_refine on Fri Aug 2 22:15:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/08_2024/8uo4_42427.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/08_2024/8uo4_42427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/08_2024/8uo4_42427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/08_2024/8uo4_42427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/08_2024/8uo4_42427.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/08_2024/8uo4_42427.cif" } resolution = 4.0 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= 0.015 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 16 5.16 5 C 3576 2.51 5 N 1034 2.21 5 O 1072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5702 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 1854 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 7, 'TRANS': 284} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 610 Unresolved non-hydrogen angles: 758 Unresolved non-hydrogen dihedrals: 495 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 13, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 27, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 392 Chain: "B" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2224 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 20, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 241 Chain: "G" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 307 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "R" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1269 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 809 Unresolved non-hydrogen dihedrals: 514 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 15, 'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 309 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.69 Number of scatterers: 5702 At special positions: 0 Unit cell: (85.0346, 137.097, 100.653, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 P 3 15.00 Mg 1 11.99 O 1072 8.00 N 1034 7.00 C 3576 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=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1732 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 44.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 9 through 40 removed outlier: 3.915A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 removed outlier: 3.813A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.601A pdb=" N ASN A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 157 removed outlier: 3.505A pdb=" N ALA A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.825A pdb=" N GLU A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.561A pdb=" N ASN A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.866A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.643A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.906A pdb=" N HIS A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 4.189A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 32 through 44 Processing helix chain 'R' and resid 36 through 55 removed outlier: 3.744A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 91 removed outlier: 3.853A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.509A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 171 removed outlier: 3.569A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 184 removed outlier: 3.927A pdb=" N ASN R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 179 through 184' Processing helix chain 'R' and resid 198 through 208 Processing helix chain 'R' and resid 209 through 234 removed outlier: 4.092A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 296 removed outlier: 4.040A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.962A pdb=" N HIS R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 326 removed outlier: 3.566A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU R 310 " --> pdb=" O GLU R 306 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU R 311 " --> pdb=" O VAL R 307 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN R 312 " --> pdb=" O TYR R 308 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 212 removed outlier: 3.531A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.207A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.778A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.947A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.493A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.268A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.615A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 858 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: 1.53 Time building geometry restraints manager: 2.40 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: 1959 1.34 - 1.46: 1163 1.46 - 1.58: 2638 1.58 - 1.69: 5 1.69 - 1.81: 20 Bond restraints: 5785 Sorted by residual: bond pdb=" N ILE A 383 " pdb=" CA ILE A 383 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.09e-02 8.42e+03 1.27e+01 bond pdb=" N TYR A 391 " pdb=" CA TYR A 391 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 7.00e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" N MET A 386 " pdb=" CA MET A 386 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.16e+00 bond pdb=" N ARG A 380 " pdb=" CA ARG A 380 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.06e+00 ... (remaining 5780 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.37: 152 107.37 - 114.36: 3337 114.36 - 121.35: 2917 121.35 - 128.34: 1514 128.34 - 135.32: 44 Bond angle restraints: 7964 Sorted by residual: angle pdb=" N ILE A 383 " pdb=" CA ILE A 383 " pdb=" C ILE A 383 " ideal model delta sigma weight residual 111.88 102.30 9.58 1.06e+00 8.90e-01 8.17e+01 angle pdb=" N ASN A 377 " pdb=" CA ASN A 377 " pdb=" C ASN A 377 " ideal model delta sigma weight residual 111.71 105.31 6.40 1.15e+00 7.56e-01 3.09e+01 angle pdb=" PB GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sigma weight residual 120.50 135.32 -14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" CA GLN A 390 " pdb=" C GLN A 390 " pdb=" O GLN A 390 " ideal model delta sigma weight residual 121.84 116.75 5.09 1.16e+00 7.43e-01 1.92e+01 angle pdb=" N GLU A 392 " pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 109.96 103.66 6.30 1.49e+00 4.50e-01 1.79e+01 ... (remaining 7959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.19: 3274 29.19 - 58.39: 51 58.39 - 87.58: 3 87.58 - 116.77: 1 116.77 - 145.97: 1 Dihedral angle restraints: 3330 sinusoidal: 687 harmonic: 2643 Sorted by residual: 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 -41.37 145.97 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 150.85 110.02 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" CA CYS A 237 " pdb=" C CYS A 237 " pdb=" N PHE A 238 " pdb=" CA PHE A 238 " ideal model delta harmonic sigma weight residual 180.00 162.73 17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 883 0.067 - 0.133: 100 0.133 - 0.200: 5 0.200 - 0.266: 3 0.266 - 0.333: 1 Chirality restraints: 992 Sorted by residual: chirality pdb=" CA ILE A 383 " pdb=" N ILE A 383 " pdb=" C ILE A 383 " pdb=" CB ILE A 383 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 382 " pdb=" N ILE A 382 " pdb=" C ILE A 382 " pdb=" CB ILE A 382 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 989 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 376 " 0.012 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C PHE A 376 " -0.044 2.00e-02 2.50e+03 pdb=" O PHE A 376 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 377 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 382 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C ILE A 382 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 382 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 383 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO G 49 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.021 5.00e-02 4.00e+02 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2040 2.84 - 3.35: 5330 3.35 - 3.87: 8398 3.87 - 4.38: 8555 4.38 - 4.90: 14978 Nonbonded interactions: 39301 Sorted by model distance: nonbonded pdb=" O SER G 31 " pdb=" OG SER G 31 " model vdw 2.322 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A 54 " pdb=" OD2 ASP A 223 " model vdw 2.369 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.371 3.040 nonbonded pdb=" O GLY B 141 " pdb=" NE2 GLN B 176 " model vdw 2.374 3.120 ... (remaining 39296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 1.410 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.890 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.004 0.052 5785 Z= 0.276 Angle : 0.716 14.824 7964 Z= 0.406 Chirality : 0.045 0.333 992 Planarity : 0.003 0.037 1040 Dihedral : 11.999 145.967 1598 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 (0.29), residues: 870 helix: 1.82 (0.28), residues: 353 sheet: -1.40 (0.42), residues: 159 loop : -1.25 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.006 0.002 HIS B 54 PHE 0.012 0.001 PHE B 235 TYR 0.005 0.001 TYR B 105 ARG 0.002 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.655 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1330 time to fit residues: 15.7897 Evaluate side-chains 58 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5785 Z= 0.195 Angle : 0.511 7.206 7964 Z= 0.280 Chirality : 0.041 0.143 992 Planarity : 0.003 0.035 1040 Dihedral : 7.059 140.165 958 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.74 % Allowed : 10.06 % Favored : 87.20 % 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: -0.02 (0.29), residues: 870 helix: 1.62 (0.27), residues: 381 sheet: -1.19 (0.41), residues: 165 loop : -1.31 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.006 0.001 HIS B 54 PHE 0.011 0.001 PHE B 292 TYR 0.018 0.001 TYR B 124 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.651 Fit side-chains REVERT: B 339 TRP cc_start: 0.8638 (OUTLIER) cc_final: 0.8246 (m-10) REVERT: G 41 CYS cc_start: 0.8147 (m) cc_final: 0.7677 (p) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.0893 time to fit residues: 9.3167 Evaluate side-chains 67 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 285 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 5785 Z= 0.322 Angle : 0.564 6.659 7964 Z= 0.311 Chirality : 0.042 0.140 992 Planarity : 0.004 0.041 1040 Dihedral : 7.105 137.172 958 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.96 % Allowed : 10.98 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.28), residues: 870 helix: 1.38 (0.27), residues: 380 sheet: -1.21 (0.41), residues: 162 loop : -1.45 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.008 0.002 HIS B 54 PHE 0.015 0.002 PHE B 235 TYR 0.018 0.002 TYR A 360 ARG 0.004 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.675 Fit side-chains REVERT: B 234 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8024 (m-80) outliers start: 13 outliers final: 9 residues processed: 62 average time/residue: 0.0888 time to fit residues: 9.3422 Evaluate side-chains 64 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 285 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.9980 chunk 42 optimal weight: 0.0570 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 5785 Z= 0.139 Angle : 0.445 6.482 7964 Z= 0.242 Chirality : 0.040 0.132 992 Planarity : 0.003 0.035 1040 Dihedral : 6.546 130.871 958 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.74 % Allowed : 13.11 % Favored : 84.15 % 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: 0.11 (0.29), residues: 870 helix: 1.86 (0.28), residues: 379 sheet: -1.29 (0.42), residues: 162 loop : -1.31 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 234 HIS 0.004 0.001 HIS B 54 PHE 0.008 0.001 PHE A 212 TYR 0.009 0.001 TYR B 124 ARG 0.002 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.685 Fit side-chains REVERT: B 234 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: B 339 TRP cc_start: 0.8579 (m100) cc_final: 0.7987 (m-10) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.0951 time to fit residues: 10.3589 Evaluate side-chains 63 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 17 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 5785 Z= 0.168 Angle : 0.448 6.240 7964 Z= 0.243 Chirality : 0.040 0.129 992 Planarity : 0.003 0.036 1040 Dihedral : 6.317 125.902 958 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.66 % Allowed : 13.41 % Favored : 82.93 % 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: 0.26 (0.29), residues: 870 helix: 2.02 (0.28), residues: 380 sheet: -1.25 (0.41), residues: 167 loop : -1.27 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.004 0.001 HIS B 54 PHE 0.010 0.001 PHE B 235 TYR 0.009 0.001 TYR B 124 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.648 Fit side-chains REVERT: B 234 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.7750 (m-80) outliers start: 12 outliers final: 9 residues processed: 63 average time/residue: 0.0920 time to fit residues: 9.6622 Evaluate side-chains 65 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.0060 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 5785 Z= 0.171 Angle : 0.447 6.034 7964 Z= 0.240 Chirality : 0.040 0.135 992 Planarity : 0.003 0.035 1040 Dihedral : 6.130 121.240 958 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.88 % Allowed : 13.11 % Favored : 82.01 % 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: 0.35 (0.29), residues: 870 helix: 2.11 (0.28), residues: 380 sheet: -1.21 (0.41), residues: 165 loop : -1.26 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE B 292 TYR 0.009 0.001 TYR A 360 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.645 Fit side-chains REVERT: B 234 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.7723 (m-80) outliers start: 16 outliers final: 11 residues processed: 69 average time/residue: 0.1070 time to fit residues: 11.4674 Evaluate side-chains 68 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 48 optimal weight: 0.0170 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5785 Z= 0.133 Angle : 0.435 6.062 7964 Z= 0.234 Chirality : 0.039 0.126 992 Planarity : 0.003 0.033 1040 Dihedral : 5.888 116.839 958 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.35 % Allowed : 14.63 % Favored : 82.01 % 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 (0.30), residues: 870 helix: 2.22 (0.28), residues: 381 sheet: -1.19 (0.41), residues: 165 loop : -1.20 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.002 0.001 HIS B 54 PHE 0.008 0.001 PHE A 212 TYR 0.008 0.001 TYR B 124 ARG 0.007 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.699 Fit side-chains REVERT: B 61 MET cc_start: 0.9099 (ppp) cc_final: 0.8353 (ppp) REVERT: B 234 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.7566 (m-80) outliers start: 11 outliers final: 9 residues processed: 67 average time/residue: 0.1056 time to fit residues: 10.9485 Evaluate side-chains 69 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 5785 Z= 0.318 Angle : 0.541 5.951 7964 Z= 0.293 Chirality : 0.042 0.133 992 Planarity : 0.004 0.045 1040 Dihedral : 6.308 119.070 958 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.66 % Allowed : 15.85 % Favored : 80.49 % 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: 0.13 (0.29), residues: 870 helix: 1.87 (0.27), residues: 381 sheet: -1.21 (0.41), residues: 160 loop : -1.37 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 297 HIS 0.005 0.001 HIS B 91 PHE 0.022 0.002 PHE B 292 TYR 0.017 0.002 TYR A 360 ARG 0.004 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.646 Fit side-chains REVERT: B 234 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.7751 (m-80) outliers start: 12 outliers final: 11 residues processed: 63 average time/residue: 0.1054 time to fit residues: 10.4417 Evaluate side-chains 67 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 5785 Z= 0.152 Angle : 0.449 5.911 7964 Z= 0.241 Chirality : 0.039 0.127 992 Planarity : 0.003 0.035 1040 Dihedral : 5.950 115.402 958 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.96 % Allowed : 17.38 % Favored : 78.66 % 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: 0.39 (0.29), residues: 870 helix: 2.14 (0.28), residues: 381 sheet: -1.19 (0.41), residues: 159 loop : -1.24 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.003 0.001 HIS B 54 PHE 0.008 0.001 PHE A 212 TYR 0.008 0.001 TYR B 124 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.638 Fit side-chains REVERT: B 234 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7668 (m-80) outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 0.1060 time to fit residues: 11.0035 Evaluate side-chains 68 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 82 optimal weight: 0.0010 chunk 71 optimal weight: 0.0070 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.0370 chunk 21 optimal weight: 0.9980 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5785 Z= 0.113 Angle : 0.429 6.071 7964 Z= 0.227 Chirality : 0.039 0.126 992 Planarity : 0.003 0.031 1040 Dihedral : 5.494 107.518 958 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.05 % Allowed : 17.68 % Favored : 79.27 % 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: 0.60 (0.30), residues: 870 helix: 2.40 (0.28), residues: 375 sheet: -0.99 (0.42), residues: 159 loop : -1.22 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 277 HIS 0.002 0.001 HIS A 220 PHE 0.007 0.001 PHE A 212 TYR 0.008 0.001 TYR B 124 ARG 0.002 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.624 Fit side-chains REVERT: B 61 MET cc_start: 0.9127 (ppp) cc_final: 0.8377 (ppp) REVERT: B 234 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7631 (m-80) outliers start: 10 outliers final: 6 residues processed: 68 average time/residue: 0.1056 time to fit residues: 11.0401 Evaluate side-chains 66 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 0.0970 chunk 29 optimal weight: 30.0000 chunk 73 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.087527 restraints weight = 16034.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.087306 restraints weight = 12875.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088211 restraints weight = 11577.988| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 5785 Z= 0.406 Angle : 0.599 6.463 7964 Z= 0.325 Chirality : 0.043 0.137 992 Planarity : 0.004 0.077 1040 Dihedral : 6.248 113.208 958 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.96 % Allowed : 16.77 % Favored : 79.27 % 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: 0.02 (0.29), residues: 870 helix: 1.79 (0.27), residues: 381 sheet: -1.39 (0.40), residues: 161 loop : -1.36 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP B 297 HIS 0.006 0.002 HIS B 91 PHE 0.032 0.003 PHE B 292 TYR 0.024 0.002 TYR A 360 ARG 0.004 0.001 ARG B 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1213.22 seconds wall clock time: 22 minutes 16.76 seconds (1336.76 seconds total)