Starting phenix.real_space_refine on Sun Nov 17 05:02:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pz2_18035/11_2024/8pz2_18035.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pz2_18035/11_2024/8pz2_18035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pz2_18035/11_2024/8pz2_18035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pz2_18035/11_2024/8pz2_18035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pz2_18035/11_2024/8pz2_18035.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pz2_18035/11_2024/8pz2_18035.cif" } resolution = 4.2 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= 0.001 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 8240 2.51 5 N 2258 2.21 5 O 2579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13121 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6188 Classifications: {'peptide': 783} Link IDs: {'PTRANS': 29, 'TRANS': 753} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2777 Classifications: {'peptide': 369} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 357} Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 440 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1760 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1263 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Time building chain proxies: 8.10, per 1000 atoms: 0.62 Number of scatterers: 13121 At special positions: 0 Unit cell: (138.45, 101.53, 125.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2579 8.00 N 2258 7.00 C 8240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.8 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3086 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 20 sheets defined 29.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 57 through 69 removed outlier: 4.196A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.581A pdb=" N GLN A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.619A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.055A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 233 removed outlier: 3.609A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.642A pdb=" N ILE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.843A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 378 through 392 removed outlier: 4.102A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 removed outlier: 5.361A pdb=" N ASN A 731 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.597A pdb=" N LEU C 42 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU C 43 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.570A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 4.382A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.562A pdb=" N VAL D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 removed outlier: 4.247A pdb=" N ARG D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.617A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 removed outlier: 3.701A pdb=" N ASP D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.548A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 4.996A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.676A pdb=" N LYS E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 49 removed outlier: 4.115A pdb=" N GLN F 47 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 57 removed outlier: 3.860A pdb=" N GLN F 55 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 88 removed outlier: 3.597A pdb=" N MET F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.704A pdb=" N LEU F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 150 removed outlier: 3.680A pdb=" N ILE F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG F 142 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN F 143 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 164 Processing helix chain 'F' and resid 396 through 420 removed outlier: 3.678A pdb=" N ALA F 419 " --> pdb=" O GLN F 415 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER F 420 " --> pdb=" O GLU F 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.735A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 6.386A pdb=" N VAL A 163 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A 96 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 181 removed outlier: 4.668A pdb=" N ILE A 177 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL A 256 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN A 179 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 258 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASN A 181 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE A 260 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 253 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU A 247 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR A 255 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL A 245 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 239 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.804A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.804A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 334 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 327 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 355 removed outlier: 5.994A pdb=" N VAL A 412 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS A 351 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 414 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 426 Processing sheet with id=AA8, first strand: chain 'A' and resid 424 through 426 removed outlier: 3.615A pdb=" N PHE A 490 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 510 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.461A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.890A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.547A pdb=" N ALA B 66 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.147A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB5, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.746A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.584A pdb=" N VAL B 252 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 286 through 291 removed outlier: 5.154A pdb=" N ASP B 288 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 299 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.781A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 33 removed outlier: 4.154A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 33 removed outlier: 6.523A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.905A pdb=" N VAL F 32 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL F 31 " --> pdb=" O LYS F 424 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS F 424 " --> pdb=" O VAL F 31 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1620 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: 4.65 Time building geometry restraints manager: 3.96 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: 4428 1.34 - 1.46: 2664 1.46 - 1.58: 6210 1.58 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 13385 Sorted by residual: bond pdb=" CB PHE A 395 " pdb=" CG PHE A 395 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.15e+00 bond pdb=" CB ASP A 740 " pdb=" CG ASP A 740 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" CG LEU A 365 " pdb=" CD2 LEU A 365 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CG ARG B 195 " pdb=" CD ARG B 195 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CG LEU B 261 " pdb=" CD2 LEU B 261 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 ... (remaining 13380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 17641 1.81 - 3.62: 467 3.62 - 5.42: 62 5.42 - 7.23: 3 7.23 - 9.04: 2 Bond angle restraints: 18175 Sorted by residual: angle pdb=" N ALA C 54 " pdb=" CA ALA C 54 " pdb=" C ALA C 54 " ideal model delta sigma weight residual 109.15 113.73 -4.58 1.44e+00 4.82e-01 1.01e+01 angle pdb=" C VAL A 532 " pdb=" N HIS A 533 " pdb=" CA HIS A 533 " ideal model delta sigma weight residual 122.62 117.84 4.78 1.56e+00 4.11e-01 9.39e+00 angle pdb=" C THR A 479 " pdb=" N VAL A 480 " pdb=" CA VAL A 480 " ideal model delta sigma weight residual 121.97 116.74 5.23 1.80e+00 3.09e-01 8.45e+00 angle pdb=" N GLY A 429 " pdb=" CA GLY A 429 " pdb=" C GLY A 429 " ideal model delta sigma weight residual 110.63 114.70 -4.07 1.43e+00 4.89e-01 8.10e+00 angle pdb=" CB LEU B 261 " pdb=" CG LEU B 261 " pdb=" CD2 LEU B 261 " ideal model delta sigma weight residual 110.70 102.51 8.19 3.00e+00 1.11e-01 7.46e+00 ... (remaining 18170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7162 17.85 - 35.70: 655 35.70 - 53.55: 118 53.55 - 71.40: 17 71.40 - 89.25: 21 Dihedral angle restraints: 7973 sinusoidal: 3135 harmonic: 4838 Sorted by residual: dihedral pdb=" CA SER B 191 " pdb=" C SER B 191 " pdb=" N LEU B 192 " pdb=" CA LEU B 192 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA THR B 386 " pdb=" C THR B 386 " pdb=" N VAL B 387 " pdb=" CA VAL B 387 " ideal model delta harmonic sigma weight residual -180.00 -156.21 -23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA VAL A 480 " pdb=" C VAL A 480 " pdb=" N ASP A 481 " pdb=" CA ASP A 481 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 7970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1431 0.047 - 0.094: 444 0.094 - 0.140: 108 0.140 - 0.187: 8 0.187 - 0.234: 4 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CA PHE A 394 " pdb=" N PHE A 394 " pdb=" C PHE A 394 " pdb=" CB PHE A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA PHE A 586 " pdb=" N PHE A 586 " pdb=" C PHE A 586 " pdb=" CB PHE A 586 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL A 364 " pdb=" CA VAL A 364 " pdb=" CG1 VAL A 364 " pdb=" CG2 VAL A 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1992 not shown) Planarity restraints: 2399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 78 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C GLN F 78 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN F 78 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE F 79 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 30 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO D 31 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 31 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 31 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 206 " -0.015 2.00e-02 2.50e+03 1.29e-02 4.19e+00 pdb=" CG TRP A 206 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 206 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 206 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 206 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 206 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 206 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 206 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 206 " -0.002 2.00e-02 2.50e+03 ... (remaining 2396 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 183 2.65 - 3.21: 12553 3.21 - 3.78: 19161 3.78 - 4.34: 25300 4.34 - 4.90: 42449 Nonbonded interactions: 99646 Sorted by model distance: nonbonded pdb=" OG1 THR E 94 " pdb=" OD1 ASN E 103 " model vdw 2.090 3.040 nonbonded pdb=" NE2 GLN A 384 " pdb=" OE1 GLU A 521 " model vdw 2.170 3.120 nonbonded pdb=" O GLY F 44 " pdb=" OG SER F 48 " model vdw 2.205 3.040 nonbonded pdb=" O TYR A 548 " pdb=" OG SER A 551 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR A 608 " pdb=" OE2 GLU A 650 " model vdw 2.229 3.040 ... (remaining 99641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.840 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 38.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.006 0.049 13385 Z= 0.417 Angle : 0.698 9.039 18175 Z= 0.382 Chirality : 0.048 0.234 1995 Planarity : 0.005 0.056 2399 Dihedral : 14.675 89.251 4887 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.07 % Allowed : 0.28 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1662 helix: 1.29 (0.25), residues: 420 sheet: -0.44 (0.25), residues: 392 loop : -1.84 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 206 HIS 0.010 0.002 HIS B 347 PHE 0.034 0.002 PHE A 586 TYR 0.028 0.002 TYR E 37 ARG 0.006 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 1.444 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 280 HIS cc_start: 0.7408 (m-70) cc_final: 0.7128 (m-70) REVERT: A 667 THR cc_start: 0.8460 (t) cc_final: 0.8225 (m) REVERT: A 780 LEU cc_start: 0.8905 (mt) cc_final: 0.8268 (tt) REVERT: D 52 ILE cc_start: 0.9275 (mt) cc_final: 0.8749 (mt) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.2405 time to fit residues: 64.2111 Evaluate side-chains 140 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 148 optimal weight: 0.0370 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 561 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13385 Z= 0.198 Angle : 0.544 7.851 18175 Z= 0.294 Chirality : 0.043 0.149 1995 Planarity : 0.004 0.052 2399 Dihedral : 4.473 25.195 1839 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.13 % 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: -0.81 (0.20), residues: 1662 helix: 1.50 (0.25), residues: 429 sheet: -0.50 (0.25), residues: 411 loop : -1.71 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 206 HIS 0.006 0.001 HIS A 533 PHE 0.018 0.001 PHE A 586 TYR 0.018 0.002 TYR D 184 ARG 0.004 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 1.678 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 76 CYS cc_start: 0.8020 (m) cc_final: 0.7755 (m) REVERT: A 667 THR cc_start: 0.8503 (t) cc_final: 0.8268 (m) REVERT: A 780 LEU cc_start: 0.8892 (mt) cc_final: 0.8246 (tt) REVERT: A 804 PHE cc_start: 0.7940 (t80) cc_final: 0.7606 (t80) REVERT: C 34 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7936 (mm-40) REVERT: D 112 ARG cc_start: 0.8207 (ttt-90) cc_final: 0.7862 (ttt-90) outliers start: 2 outliers final: 1 residues processed: 188 average time/residue: 0.2665 time to fit residues: 73.5052 Evaluate side-chains 149 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 561 GLN B 186 ASN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13385 Z= 0.395 Angle : 0.637 7.533 18175 Z= 0.342 Chirality : 0.046 0.173 1995 Planarity : 0.005 0.065 2399 Dihedral : 4.811 25.127 1839 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.14 % Allowed : 5.10 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1662 helix: 1.27 (0.25), residues: 434 sheet: -0.62 (0.25), residues: 398 loop : -1.89 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 206 HIS 0.007 0.001 HIS A 533 PHE 0.031 0.002 PHE A 586 TYR 0.024 0.002 TYR E 37 ARG 0.006 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 1.606 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 296 TYR cc_start: 0.8907 (t80) cc_final: 0.8686 (t80) REVERT: A 780 LEU cc_start: 0.8913 (mt) cc_final: 0.8251 (tt) REVERT: C 34 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7975 (mm-40) REVERT: D 31 PRO cc_start: 0.8773 (Cg_exo) cc_final: 0.8492 (Cg_endo) REVERT: D 52 ILE cc_start: 0.9268 (mt) cc_final: 0.8775 (mt) REVERT: D 112 ARG cc_start: 0.8354 (ttt-90) cc_final: 0.8096 (ttt-90) outliers start: 2 outliers final: 1 residues processed: 185 average time/residue: 0.2527 time to fit residues: 68.7111 Evaluate side-chains 143 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 259 ASN A 561 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13385 Z= 0.155 Angle : 0.524 8.046 18175 Z= 0.282 Chirality : 0.043 0.168 1995 Planarity : 0.004 0.061 2399 Dihedral : 4.285 24.143 1839 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % 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: -0.77 (0.21), residues: 1662 helix: 1.66 (0.25), residues: 428 sheet: -0.51 (0.25), residues: 405 loop : -1.73 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.004 0.001 HIS A 533 PHE 0.025 0.001 PHE A 586 TYR 0.019 0.001 TYR D 184 ARG 0.003 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.566 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 780 LEU cc_start: 0.8891 (mt) cc_final: 0.8261 (tt) REVERT: B 285 SER cc_start: 0.8283 (p) cc_final: 0.8043 (p) REVERT: C 34 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7970 (mm-40) REVERT: D 104 ASN cc_start: 0.8675 (m-40) cc_final: 0.8384 (m-40) REVERT: D 146 ASP cc_start: 0.7921 (m-30) cc_final: 0.7085 (m-30) REVERT: D 205 TYR cc_start: 0.8970 (m-10) cc_final: 0.8735 (m-10) REVERT: F 87 MET cc_start: 0.7963 (tpt) cc_final: 0.7454 (tpp) outliers start: 1 outliers final: 1 residues processed: 198 average time/residue: 0.2597 time to fit residues: 77.9107 Evaluate side-chains 153 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 2 optimal weight: 0.0000 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13385 Z= 0.259 Angle : 0.567 8.827 18175 Z= 0.303 Chirality : 0.044 0.151 1995 Planarity : 0.004 0.060 2399 Dihedral : 4.427 24.395 1839 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1662 helix: 1.59 (0.25), residues: 430 sheet: -0.49 (0.26), residues: 402 loop : -1.79 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 183 HIS 0.005 0.001 HIS A 533 PHE 0.026 0.002 PHE A 586 TYR 0.020 0.002 TYR E 37 ARG 0.004 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.615 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 420 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8631 (mt-10) REVERT: A 780 LEU cc_start: 0.8896 (mt) cc_final: 0.8242 (tt) REVERT: C 34 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7913 (mm-40) REVERT: D 52 ILE cc_start: 0.9206 (mt) cc_final: 0.8812 (mt) REVERT: F 87 MET cc_start: 0.7836 (tpt) cc_final: 0.7347 (tpp) outliers start: 1 outliers final: 1 residues processed: 189 average time/residue: 0.2527 time to fit residues: 70.1885 Evaluate side-chains 147 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13385 Z= 0.328 Angle : 0.615 8.290 18175 Z= 0.329 Chirality : 0.046 0.200 1995 Planarity : 0.005 0.059 2399 Dihedral : 4.669 25.310 1839 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.10 % 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: -0.99 (0.21), residues: 1662 helix: 1.30 (0.25), residues: 440 sheet: -0.59 (0.26), residues: 399 loop : -1.83 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.006 0.001 HIS A 533 PHE 0.026 0.002 PHE A 586 TYR 0.023 0.002 TYR E 37 ARG 0.007 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 85 LEU cc_start: 0.8585 (tp) cc_final: 0.8370 (mm) REVERT: A 780 LEU cc_start: 0.8923 (mt) cc_final: 0.8244 (tt) REVERT: C 34 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7926 (mm-40) REVERT: E 66 ASP cc_start: 0.8961 (t0) cc_final: 0.8714 (t0) REVERT: F 83 MET cc_start: 0.9086 (ttm) cc_final: 0.8754 (tpp) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.2526 time to fit residues: 68.8903 Evaluate side-chains 145 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 98 optimal weight: 0.0870 chunk 96 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS B 170 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13385 Z= 0.223 Angle : 0.566 8.793 18175 Z= 0.301 Chirality : 0.044 0.165 1995 Planarity : 0.004 0.057 2399 Dihedral : 4.485 25.561 1839 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.14 % Allowed : 1.77 % Favored : 98.09 % 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: -0.85 (0.21), residues: 1662 helix: 1.49 (0.25), residues: 433 sheet: -0.52 (0.26), residues: 397 loop : -1.76 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 206 HIS 0.005 0.001 HIS A 533 PHE 0.021 0.001 PHE A 586 TYR 0.020 0.002 TYR E 37 ARG 0.006 0.000 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 194 time to evaluate : 1.502 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 91 ARG cc_start: 0.6802 (mtt-85) cc_final: 0.6600 (mtt180) REVERT: A 780 LEU cc_start: 0.8883 (mt) cc_final: 0.8229 (tt) REVERT: B 31 LYS cc_start: 0.8108 (pttt) cc_final: 0.7670 (mtmt) REVERT: B 368 GLN cc_start: 0.8758 (pp30) cc_final: 0.8395 (pp30) REVERT: B 388 TYR cc_start: 0.7662 (m-80) cc_final: 0.7125 (m-80) REVERT: D 52 ILE cc_start: 0.9244 (mt) cc_final: 0.8800 (mt) REVERT: E 66 ASP cc_start: 0.8962 (t0) cc_final: 0.8718 (t0) REVERT: F 76 MET cc_start: 0.7753 (tpp) cc_final: 0.7086 (tmm) REVERT: F 77 ASP cc_start: 0.7624 (m-30) cc_final: 0.7138 (m-30) REVERT: F 83 MET cc_start: 0.9054 (ttm) cc_final: 0.8697 (tpp) outliers start: 2 outliers final: 1 residues processed: 196 average time/residue: 0.2421 time to fit residues: 70.4837 Evaluate side-chains 154 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 0.0030 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13385 Z= 0.285 Angle : 0.602 9.258 18175 Z= 0.320 Chirality : 0.045 0.164 1995 Planarity : 0.005 0.058 2399 Dihedral : 4.597 24.534 1839 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.14 % Allowed : 1.20 % Favored : 98.66 % 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: -0.93 (0.21), residues: 1662 helix: 1.47 (0.25), residues: 430 sheet: -0.53 (0.25), residues: 408 loop : -1.86 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 206 HIS 0.006 0.001 HIS A 533 PHE 0.023 0.002 PHE A 586 TYR 0.026 0.002 TYR A 230 ARG 0.005 0.000 ARG E 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 1.860 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 89 LYS cc_start: 0.8612 (tppt) cc_final: 0.8127 (tppt) REVERT: A 422 ASN cc_start: 0.8326 (t0) cc_final: 0.8121 (t0) REVERT: A 780 LEU cc_start: 0.8906 (mt) cc_final: 0.8232 (tt) REVERT: B 31 LYS cc_start: 0.8110 (pttt) cc_final: 0.7710 (mtmt) REVERT: B 388 TYR cc_start: 0.7733 (m-80) cc_final: 0.7184 (m-80) REVERT: C 43 GLU cc_start: 0.7130 (mp0) cc_final: 0.6908 (mp0) REVERT: D 146 ASP cc_start: 0.7783 (m-30) cc_final: 0.7347 (m-30) REVERT: E 66 ASP cc_start: 0.8949 (t0) cc_final: 0.8701 (t0) REVERT: F 83 MET cc_start: 0.9064 (ttm) cc_final: 0.8680 (tpp) REVERT: F 87 MET cc_start: 0.7802 (tpt) cc_final: 0.7437 (tpt) outliers start: 2 outliers final: 1 residues processed: 193 average time/residue: 0.2632 time to fit residues: 75.1774 Evaluate side-chains 148 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13385 Z= 0.218 Angle : 0.571 9.252 18175 Z= 0.303 Chirality : 0.044 0.175 1995 Planarity : 0.004 0.058 2399 Dihedral : 4.463 26.076 1839 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.14 % Allowed : 0.71 % Favored : 99.15 % 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: -0.78 (0.21), residues: 1662 helix: 1.62 (0.25), residues: 424 sheet: -0.47 (0.25), residues: 407 loop : -1.74 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.006 0.001 HIS A 30 PHE 0.021 0.001 PHE A 586 TYR 0.022 0.001 TYR A 230 ARG 0.005 0.000 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 1.602 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 76 CYS cc_start: 0.7821 (m) cc_final: 0.7552 (m) REVERT: A 89 LYS cc_start: 0.8584 (tppt) cc_final: 0.8053 (tppt) REVERT: A 768 MET cc_start: 0.6734 (tmm) cc_final: 0.6487 (tmm) REVERT: A 780 LEU cc_start: 0.8898 (mt) cc_final: 0.8231 (tt) REVERT: B 31 LYS cc_start: 0.8101 (pttt) cc_final: 0.7782 (mtmt) REVERT: B 388 TYR cc_start: 0.7639 (m-80) cc_final: 0.7123 (m-80) REVERT: C 43 GLU cc_start: 0.7093 (mp0) cc_final: 0.6862 (mp0) REVERT: D 52 ILE cc_start: 0.9195 (mt) cc_final: 0.8751 (mt) REVERT: D 146 ASP cc_start: 0.7948 (m-30) cc_final: 0.7460 (m-30) REVERT: E 66 ASP cc_start: 0.8893 (t0) cc_final: 0.8630 (t0) REVERT: F 76 MET cc_start: 0.7806 (tpp) cc_final: 0.7186 (tmm) REVERT: F 83 MET cc_start: 0.9046 (ttm) cc_final: 0.8639 (tpp) REVERT: F 87 MET cc_start: 0.7819 (tpt) cc_final: 0.7461 (tpt) outliers start: 2 outliers final: 1 residues processed: 190 average time/residue: 0.2593 time to fit residues: 72.3723 Evaluate side-chains 150 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 95 optimal weight: 0.0570 chunk 73 optimal weight: 0.4980 chunk 108 optimal weight: 0.0980 chunk 163 optimal weight: 5.9990 chunk 150 optimal weight: 0.1980 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS D 89 GLN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13385 Z= 0.143 Angle : 0.540 9.282 18175 Z= 0.285 Chirality : 0.043 0.174 1995 Planarity : 0.004 0.059 2399 Dihedral : 4.108 24.352 1839 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.14 % Allowed : 0.21 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1662 helix: 1.81 (0.25), residues: 423 sheet: -0.47 (0.25), residues: 435 loop : -1.64 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 413 HIS 0.005 0.001 HIS A 30 PHE 0.016 0.001 PHE A 586 TYR 0.022 0.001 TYR E 37 ARG 0.005 0.000 ARG A 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 1.575 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 76 CYS cc_start: 0.7717 (m) cc_final: 0.7462 (m) REVERT: A 89 LYS cc_start: 0.8555 (tppt) cc_final: 0.8017 (tppt) REVERT: A 667 THR cc_start: 0.8377 (t) cc_final: 0.8027 (m) REVERT: A 780 LEU cc_start: 0.8903 (mt) cc_final: 0.8256 (tt) REVERT: C 31 TYR cc_start: 0.6654 (p90) cc_final: 0.6450 (p90) REVERT: D 104 ASN cc_start: 0.8578 (m-40) cc_final: 0.8370 (m-40) REVERT: E 66 ASP cc_start: 0.8829 (t0) cc_final: 0.8525 (t70) REVERT: F 76 MET cc_start: 0.7825 (tpp) cc_final: 0.7257 (tmm) REVERT: F 83 MET cc_start: 0.9043 (ttm) cc_final: 0.8664 (tpp) outliers start: 2 outliers final: 1 residues processed: 203 average time/residue: 0.2512 time to fit residues: 75.8037 Evaluate side-chains 166 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 533 HIS ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.087743 restraints weight = 26484.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.086806 restraints weight = 26245.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.087699 restraints weight = 29521.572| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13385 Z= 0.197 Angle : 0.559 9.112 18175 Z= 0.294 Chirality : 0.044 0.163 1995 Planarity : 0.004 0.058 2399 Dihedral : 4.189 24.862 1839 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.14 % Allowed : 0.42 % Favored : 99.43 % 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: -0.59 (0.21), residues: 1662 helix: 1.81 (0.25), residues: 422 sheet: -0.39 (0.25), residues: 423 loop : -1.63 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 206 HIS 0.004 0.001 HIS A 30 PHE 0.020 0.001 PHE A 586 TYR 0.029 0.001 TYR A 230 ARG 0.003 0.000 ARG B 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2534.70 seconds wall clock time: 47 minutes 17.20 seconds (2837.20 seconds total)