Starting phenix.real_space_refine on Fri Jul 19 01:59:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/07_2024/8uo4_42427_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/07_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_42427/07_2024/8uo4_42427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/07_2024/8uo4_42427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/07_2024/8uo4_42427_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo4_42427/07_2024/8uo4_42427_neut.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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.57, per 1000 atoms: 0.80 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: 2.49 Conformation dependent library (CDL) restraints added in 1.3 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: 0.72 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: 1.68 Time building geometry restraints manager: 2.73 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 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.345 2.440 nonbonded pdb=" OG SER A 54 " pdb=" OD2 ASP A 223 " model vdw 2.369 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.371 2.440 nonbonded pdb=" O GLY B 141 " pdb=" NE2 GLN B 176 " model vdw 2.374 2.520 ... (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 ========== 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: 1.750 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: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.980 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- 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 : 0.648 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1323 time to fit residues: 15.7509 Evaluate side-chains 58 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.0030 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- 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: 0.7852 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 5785 Z= 0.163 Angle : 0.488 6.397 7964 Z= 0.266 Chirality : 0.041 0.150 992 Planarity : 0.003 0.033 1040 Dihedral : 6.920 138.736 958 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.74 % Allowed : 9.15 % Favored : 88.11 % 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 (0.29), residues: 870 helix: 1.76 (0.27), residues: 374 sheet: -1.22 (0.43), residues: 156 loop : -1.31 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 277 HIS 0.006 0.001 HIS B 54 PHE 0.008 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 74 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.665 Fit side-chains REVERT: B 339 TRP cc_start: 0.8619 (OUTLIER) cc_final: 0.8328 (m-10) REVERT: G 41 CYS cc_start: 0.8080 (m) cc_final: 0.7610 (p) outliers start: 9 outliers final: 8 residues processed: 69 average time/residue: 0.0918 time to fit residues: 10.3112 Evaluate side-chains 68 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 264 ASN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7910 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5785 Z= 0.214 Angle : 0.483 5.982 7964 Z= 0.263 Chirality : 0.040 0.135 992 Planarity : 0.003 0.035 1040 Dihedral : 6.595 132.496 958 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.18 % Allowed : 10.06 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.29), residues: 870 helix: 1.74 (0.27), residues: 380 sheet: -1.11 (0.41), residues: 162 loop : -1.32 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.007 0.002 HIS B 54 PHE 0.016 0.001 PHE B 292 TYR 0.014 0.001 TYR B 124 ARG 0.002 0.000 ARG A 317 *********************** 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 76 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.651 Fit side-chains REVERT: B 234 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.7955 (m-80) outliers start: 17 outliers final: 14 residues processed: 68 average time/residue: 0.0908 time to fit residues: 10.2364 Evaluate side-chains 71 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 72 SER 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 159 THR 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: 5.9990 chunk 9 optimal weight: 0.0570 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 0.0000 chunk 72 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.5902 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5785 Z= 0.121 Angle : 0.424 5.919 7964 Z= 0.229 Chirality : 0.039 0.128 992 Planarity : 0.003 0.031 1040 Dihedral : 6.156 125.590 958 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.13 % Allowed : 14.02 % Favored : 83.84 % 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: 0.36 (0.29), residues: 870 helix: 2.07 (0.28), residues: 381 sheet: -1.12 (0.41), residues: 170 loop : -1.24 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 234 HIS 0.003 0.001 HIS B 54 PHE 0.009 0.001 PHE B 292 TYR 0.010 0.001 TYR B 124 ARG 0.002 0.000 ARG A 232 *********************** 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 73 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.675 Fit side-chains REVERT: A 234 TRP cc_start: 0.8427 (p90) cc_final: 0.8194 (p-90) REVERT: B 234 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: B 339 TRP cc_start: 0.8546 (m100) cc_final: 0.8110 (m-10) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.1119 time to fit residues: 11.9570 Evaluate side-chains 67 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 234 PHE 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: 1.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 17 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5785 Z= 0.208 Angle : 0.464 5.860 7964 Z= 0.251 Chirality : 0.040 0.131 992 Planarity : 0.003 0.035 1040 Dihedral : 6.161 123.502 958 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 6.10 % Allowed : 12.20 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.29), residues: 870 helix: 2.08 (0.27), residues: 381 sheet: -1.08 (0.41), residues: 165 loop : -1.22 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 297 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE B 235 TYR 0.010 0.001 TYR A 360 ARG 0.002 0.000 ARG B 150 *********************** 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 79 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.546 Fit side-chains REVERT: B 234 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: B 339 TRP cc_start: 0.8609 (m100) cc_final: 0.8082 (m-10) outliers start: 20 outliers final: 14 residues processed: 71 average time/residue: 0.0898 time to fit residues: 10.3043 Evaluate side-chains 73 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 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 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 118 THR 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: 0.3980 chunk 21 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7854 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5785 Z= 0.122 Angle : 0.429 6.456 7964 Z= 0.227 Chirality : 0.039 0.150 992 Planarity : 0.003 0.032 1040 Dihedral : 5.888 119.059 958 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.96 % Allowed : 15.55 % 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: 0.56 (0.29), residues: 870 helix: 2.27 (0.28), residues: 382 sheet: -0.98 (0.41), residues: 168 loop : -1.21 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 234 HIS 0.002 0.001 HIS B 225 PHE 0.008 0.001 PHE A 212 TYR 0.009 0.001 TYR B 124 ARG 0.001 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 79 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.666 Fit side-chains REVERT: A 234 TRP cc_start: 0.8426 (p90) cc_final: 0.8107 (p-90) REVERT: B 234 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: B 339 TRP cc_start: 0.8573 (m100) cc_final: 0.8029 (m-10) outliers start: 13 outliers final: 11 residues processed: 74 average time/residue: 0.0906 time to fit residues: 10.8609 Evaluate side-chains 75 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN 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 72 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 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: 0.5980 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7885 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5785 Z= 0.165 Angle : 0.452 7.963 7964 Z= 0.240 Chirality : 0.039 0.128 992 Planarity : 0.003 0.034 1040 Dihedral : 5.829 116.357 958 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.49 % Allowed : 14.63 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.30), residues: 870 helix: 2.29 (0.28), residues: 381 sheet: -1.00 (0.41), residues: 168 loop : -1.23 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 297 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE B 292 TYR 0.008 0.001 TYR B 124 ARG 0.002 0.000 ARG A 317 *********************** 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 80 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.638 Fit side-chains REVERT: A 234 TRP cc_start: 0.8492 (p90) cc_final: 0.8145 (p-90) REVERT: B 234 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: B 339 TRP cc_start: 0.8597 (m100) cc_final: 0.8059 (m-10) outliers start: 18 outliers final: 14 residues processed: 73 average time/residue: 0.0903 time to fit residues: 10.7174 Evaluate side-chains 77 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER 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 B residue 294 CYS Chi-restraints excluded: chain R residue 118 THR 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: 1.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 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: 1.9990 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.7909 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5785 Z= 0.202 Angle : 0.472 7.859 7964 Z= 0.252 Chirality : 0.040 0.136 992 Planarity : 0.003 0.035 1040 Dihedral : 5.892 115.092 958 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.49 % Allowed : 14.63 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.29), residues: 870 helix: 2.27 (0.28), residues: 380 sheet: -1.01 (0.43), residues: 157 loop : -1.30 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 297 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE B 235 TYR 0.010 0.001 TYR A 360 ARG 0.002 0.000 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 77 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.694 Fit side-chains REVERT: A 234 TRP cc_start: 0.8554 (p90) cc_final: 0.8240 (p-90) REVERT: B 234 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.7824 (m-80) outliers start: 18 outliers final: 15 residues processed: 71 average time/residue: 0.0883 time to fit residues: 10.2633 Evaluate side-chains 75 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 264 ASN 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 72 SER 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 B residue 294 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 118 THR 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: 10.0000 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5785 Z= 0.112 Angle : 0.433 9.042 7964 Z= 0.228 Chirality : 0.039 0.147 992 Planarity : 0.003 0.031 1040 Dihedral : 5.550 109.815 958 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.57 % Allowed : 16.16 % 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: 0.73 (0.30), residues: 870 helix: 2.41 (0.28), residues: 382 sheet: -0.81 (0.42), residues: 165 loop : -1.19 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.002 0.001 HIS A 220 PHE 0.008 0.001 PHE A 212 TYR 0.005 0.001 TYR B 59 ARG 0.002 0.000 ARG B 314 *********************** 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 83 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.654 Fit side-chains REVERT: A 234 TRP cc_start: 0.8570 (p90) cc_final: 0.8213 (p-90) REVERT: B 234 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: B 339 TRP cc_start: 0.8601 (m100) cc_final: 0.8022 (m-10) outliers start: 15 outliers final: 12 residues processed: 76 average time/residue: 0.0903 time to fit residues: 11.1346 Evaluate side-chains 76 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN 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 72 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 B residue 296 VAL Chi-restraints excluded: chain R residue 118 THR 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: 0.0870 chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 0.0870 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 0.0570 chunk 21 optimal weight: 0.5980 overall best weight: 0.3054 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5785 Z= 0.110 Angle : 0.452 11.068 7964 Z= 0.231 Chirality : 0.039 0.157 992 Planarity : 0.002 0.030 1040 Dihedral : 5.375 105.635 958 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.74 % Allowed : 18.90 % Favored : 78.35 % 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: 0.75 (0.30), residues: 870 helix: 2.45 (0.28), residues: 377 sheet: -0.69 (0.42), residues: 165 loop : -1.21 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE A 212 TYR 0.005 0.000 TYR B 289 ARG 0.001 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 73 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.644 Fit side-chains REVERT: A 234 TRP cc_start: 0.8565 (p90) cc_final: 0.8229 (p-90) REVERT: B 234 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: B 339 TRP cc_start: 0.8549 (m100) cc_final: 0.7960 (m-10) outliers start: 9 outliers final: 8 residues processed: 69 average time/residue: 0.0924 time to fit residues: 10.4943 Evaluate side-chains 73 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 30.0000 chunk 73 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 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 R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.106404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088830 restraints weight = 16268.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088581 restraints weight = 12883.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.089443 restraints weight = 11887.231| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 5785 Z= 0.325 Angle : 0.558 10.161 7964 Z= 0.295 Chirality : 0.041 0.141 992 Planarity : 0.004 0.038 1040 Dihedral : 5.841 108.527 958 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.18 % Allowed : 16.46 % Favored : 78.35 % 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: 0.39 (0.29), residues: 870 helix: 2.20 (0.27), residues: 375 sheet: -1.13 (0.41), residues: 162 loop : -1.30 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 297 HIS 0.005 0.001 HIS B 91 PHE 0.031 0.002 PHE A 222 TYR 0.018 0.002 TYR A 360 ARG 0.003 0.001 ARG B 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1290.57 seconds wall clock time: 23 minutes 44.39 seconds (1424.39 seconds total)