Starting phenix.real_space_refine on Thu Feb 15 01:05:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kau_22784/02_2024/7kau_22784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kau_22784/02_2024/7kau_22784.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/7kau_22784/02_2024/7kau_22784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kau_22784/02_2024/7kau_22784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kau_22784/02_2024/7kau_22784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kau_22784/02_2024/7kau_22784.pdb" } 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= 0.008 sd= 0.063 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 39 5.16 5 C 6981 2.51 5 N 1810 2.21 5 O 1881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 185": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10711 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3358 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 435 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 229 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 27, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'PHE:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 86 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1129 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1471 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 280 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'UNK:plan-1': 56} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 5.92, per 1000 atoms: 0.55 Number of scatterers: 10711 At special positions: 0 Unit cell: (109.48, 127.33, 138.04, 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 39 16.00 O 1881 8.00 N 1810 7.00 C 6981 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: 4.39 Conformation dependent library (CDL) restraints added in 1.8 seconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 70.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.580A pdb=" N LYS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 70 removed outlier: 3.658A pdb=" N ARG A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 107 through 137 removed outlier: 3.819A pdb=" N ARG A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.583A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.659A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.902A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.736A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 314 removed outlier: 4.114A pdb=" N ILE A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 341 through 346 removed outlier: 3.567A pdb=" N TYR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 346' Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 358 through 384 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.628A pdb=" N LYS A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 440 removed outlier: 3.630A pdb=" N GLY A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 466 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 4.219A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 3.517A pdb=" N VAL C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 82 Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.524A pdb=" N PHE D 17 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Proline residue: D 28 - end of helix Processing helix chain 'D' and resid 58 through 67 removed outlier: 4.496A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 94 through 113 removed outlier: 3.548A pdb=" N ASN D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 removed outlier: 3.572A pdb=" N GLY D 217 " --> pdb=" O PHE D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.907A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 249 removed outlier: 3.618A pdb=" N TYR D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.819A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.696A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.703A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 288 through 294' Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 3.803A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 4.030A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.335A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.664A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.263A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 486 Processing helix chain 'D' and resid 487 through 492 removed outlier: 4.273A pdb=" N MET D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'E' and resid 72 through 86 removed outlier: 3.749A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 124 removed outlier: 4.006A pdb=" N LYS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 3.652A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 182 removed outlier: 4.042A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.891A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.962A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG E 203 " --> pdb=" O ASN E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 203' Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.678A pdb=" N GLU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 4.045A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 removed outlier: 3.762A pdb=" N LYS F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 120 removed outlier: 3.663A pdb=" N GLN F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Proline residue: F 103 - end of helix Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.719A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 168 Processing helix chain 'F' and resid 175 through 192 Processing helix chain 'G' and resid 151 through 170 removed outlier: 3.598A pdb=" N UNK G 170 " --> pdb=" O UNK G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 205 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211 removed outlier: 3.511A pdb=" N GLU A 210 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 203 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 284 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 434 removed outlier: 6.842A pdb=" N LYS D 454 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA D 433 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N SER D 452 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.527A pdb=" N VAL D 590 " --> pdb=" O ILE D 604 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 604 " --> pdb=" O VAL D 590 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 592 " --> pdb=" O LEU D 602 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 602 " --> pdb=" O VAL D 592 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 678 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3390 1.34 - 1.46: 1852 1.46 - 1.57: 5615 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 10918 Sorted by residual: bond pdb=" C THR D 595 " pdb=" N ASP D 596 " ideal model delta sigma weight residual 1.332 1.316 0.016 1.40e-02 5.10e+03 1.34e+00 bond pdb=" C ILE D 425 " pdb=" N PRO D 426 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.11e-02 8.12e+03 9.83e-01 bond pdb=" CB TRP D 283 " pdb=" CG TRP D 283 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.78e-01 bond pdb=" CA GLN F 155 " pdb=" CB GLN F 155 " ideal model delta sigma weight residual 1.532 1.519 0.014 1.62e-02 3.81e+03 7.13e-01 bond pdb=" CA GLY A 176 " pdb=" C GLY A 176 " ideal model delta sigma weight residual 1.522 1.512 0.010 1.29e-02 6.01e+03 6.08e-01 ... (remaining 10913 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.46: 292 106.46 - 113.34: 6143 113.34 - 120.22: 4025 120.22 - 127.09: 4242 127.09 - 133.97: 109 Bond angle restraints: 14811 Sorted by residual: angle pdb=" N ILE E 126 " pdb=" CA ILE E 126 " pdb=" C ILE E 126 " ideal model delta sigma weight residual 113.71 109.99 3.72 9.50e-01 1.11e+00 1.53e+01 angle pdb=" N VAL E 205 " pdb=" CA VAL E 205 " pdb=" C VAL E 205 " ideal model delta sigma weight residual 111.88 108.56 3.32 1.06e+00 8.90e-01 9.80e+00 angle pdb=" CA VAL D 215 " pdb=" C VAL D 215 " pdb=" N ASP D 216 " ideal model delta sigma weight residual 116.60 120.55 -3.95 1.45e+00 4.76e-01 7.40e+00 angle pdb=" C GLU A 266 " pdb=" N LEU A 267 " pdb=" CA LEU A 267 " ideal model delta sigma weight residual 121.95 111.98 9.97 3.74e+00 7.15e-02 7.11e+00 angle pdb=" N SER A 289 " pdb=" CA SER A 289 " pdb=" C SER A 289 " ideal model delta sigma weight residual 111.11 114.24 -3.13 1.20e+00 6.94e-01 6.81e+00 ... (remaining 14806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 6066 17.36 - 34.72: 430 34.72 - 52.09: 62 52.09 - 69.45: 7 69.45 - 86.81: 8 Dihedral angle restraints: 6573 sinusoidal: 2514 harmonic: 4059 Sorted by residual: dihedral pdb=" CA VAL D 437 " pdb=" C VAL D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ILE D 425 " pdb=" C ILE D 425 " pdb=" N PRO D 426 " pdb=" CA PRO D 426 " ideal model delta harmonic sigma weight residual -180.00 -164.11 -15.89 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CB GLU D 473 " pdb=" CG GLU D 473 " pdb=" CD GLU D 473 " pdb=" OE1 GLU D 473 " ideal model delta sinusoidal sigma weight residual 0.00 -86.81 86.81 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 6570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 945 0.025 - 0.050: 540 0.050 - 0.076: 169 0.076 - 0.101: 73 0.101 - 0.126: 41 Chirality restraints: 1768 Sorted by residual: chirality pdb=" CA ILE D 470 " pdb=" N ILE D 470 " pdb=" C ILE D 470 " pdb=" CB ILE D 470 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA PRO D 375 " pdb=" N PRO D 375 " pdb=" C PRO D 375 " pdb=" CB PRO D 375 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA THR A 291 " pdb=" N THR A 291 " pdb=" C THR A 291 " pdb=" CB THR A 291 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1765 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO F 48 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 93 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO F 94 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 94 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 94 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 437 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO D 438 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 438 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 438 " -0.019 5.00e-02 4.00e+02 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2401 2.78 - 3.31: 10631 3.31 - 3.84: 16840 3.84 - 4.37: 17505 4.37 - 4.90: 31497 Nonbonded interactions: 78874 Sorted by model distance: nonbonded pdb=" OD1 ASP D 308 " pdb=" NH1 ARG D 313 " model vdw 2.251 2.520 nonbonded pdb=" OG SER A 271 " pdb=" O VAL A 274 " model vdw 2.259 2.440 nonbonded pdb=" NZ LYS D 538 " pdb=" O ASP D 565 " model vdw 2.263 2.520 nonbonded pdb=" O PHE A 198 " pdb=" OH TYR C 66 " model vdw 2.278 2.440 nonbonded pdb=" OE1 GLN D 370 " pdb=" OG1 THR D 391 " model vdw 2.283 2.440 ... (remaining 78869 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: 1.220 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: 4.110 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.610 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.003 0.027 10918 Z= 0.207 Angle : 0.559 9.970 14811 Z= 0.311 Chirality : 0.038 0.126 1768 Planarity : 0.003 0.045 1846 Dihedral : 12.117 86.810 3935 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % 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: -0.93 (0.22), residues: 1316 helix: 0.39 (0.17), residues: 808 sheet: -2.21 (0.48), residues: 82 loop : -2.18 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 380 HIS 0.003 0.001 HIS B 72 PHE 0.015 0.001 PHE A 194 TYR 0.018 0.001 TYR F 190 ARG 0.002 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9095 (mmm) cc_final: 0.8823 (mmm) REVERT: A 290 ASN cc_start: 0.8938 (m-40) cc_final: 0.8511 (p0) REVERT: A 368 PHE cc_start: 0.9524 (t80) cc_final: 0.9241 (t80) REVERT: D 102 LEU cc_start: 0.8862 (mm) cc_final: 0.8460 (mm) REVERT: D 491 MET cc_start: 0.8811 (ttp) cc_final: 0.8126 (tmm) REVERT: D 601 ASP cc_start: 0.9055 (m-30) cc_final: 0.8821 (m-30) REVERT: E 81 MET cc_start: 0.8743 (ttm) cc_final: 0.8095 (tmm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2416 time to fit residues: 37.3532 Evaluate side-chains 59 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 298 GLN D 307 GLN D 334 HIS D 424 HIS D 427 ASN D 494 GLN E 88 HIS E 123 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 GLN ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10918 Z= 0.310 Angle : 0.601 7.623 14811 Z= 0.303 Chirality : 0.040 0.158 1768 Planarity : 0.004 0.045 1846 Dihedral : 3.686 20.183 1476 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.80 % Allowed : 12.58 % Favored : 85.62 % 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 (0.24), residues: 1316 helix: 1.65 (0.18), residues: 816 sheet: -1.68 (0.48), residues: 78 loop : -1.76 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 380 HIS 0.004 0.001 HIS C 72 PHE 0.012 0.001 PHE D 343 TYR 0.021 0.002 TYR F 190 ARG 0.017 0.001 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.9064 (t70) cc_final: 0.8758 (t0) REVERT: A 249 MET cc_start: 0.9097 (mmm) cc_final: 0.8837 (mmm) REVERT: A 290 ASN cc_start: 0.9078 (m-40) cc_final: 0.8686 (p0) REVERT: A 368 PHE cc_start: 0.9550 (t80) cc_final: 0.9323 (t80) REVERT: D 102 LEU cc_start: 0.8932 (mm) cc_final: 0.8546 (mm) REVERT: D 603 ASP cc_start: 0.7307 (t0) cc_final: 0.7008 (t0) REVERT: E 81 MET cc_start: 0.8775 (ttm) cc_final: 0.8220 (tmm) outliers start: 20 outliers final: 11 residues processed: 79 average time/residue: 0.1838 time to fit residues: 23.9539 Evaluate side-chains 70 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 170 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 134 optimal weight: 40.0000 chunk 110 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 HIS ** D 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10918 Z= 0.261 Angle : 0.553 7.843 14811 Z= 0.277 Chirality : 0.039 0.132 1768 Planarity : 0.003 0.045 1846 Dihedral : 3.642 22.012 1476 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.25 % Allowed : 15.63 % Favored : 82.12 % 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: 1.33 (0.24), residues: 1316 helix: 2.20 (0.19), residues: 819 sheet: -1.09 (0.52), residues: 82 loop : -1.49 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 380 HIS 0.004 0.001 HIS E 88 PHE 0.011 0.001 PHE D 547 TYR 0.019 0.001 TYR F 190 ARG 0.003 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9106 (mmm) cc_final: 0.8841 (mmm) REVERT: A 290 ASN cc_start: 0.9110 (m-40) cc_final: 0.8734 (p0) REVERT: A 368 PHE cc_start: 0.9549 (t80) cc_final: 0.9348 (t80) REVERT: C 49 LYS cc_start: 0.9271 (ptpt) cc_final: 0.9057 (pttm) REVERT: B 72 HIS cc_start: 0.8646 (OUTLIER) cc_final: 0.7881 (m170) REVERT: D 102 LEU cc_start: 0.9004 (mm) cc_final: 0.8622 (mm) REVERT: D 603 ASP cc_start: 0.7447 (t0) cc_final: 0.7196 (t0) REVERT: D 608 MET cc_start: 0.8284 (ptt) cc_final: 0.7658 (ppp) REVERT: E 81 MET cc_start: 0.8760 (ttm) cc_final: 0.8314 (tmm) outliers start: 25 outliers final: 17 residues processed: 83 average time/residue: 0.1749 time to fit residues: 23.8154 Evaluate side-chains 71 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 chunk 65 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10918 Z= 0.304 Angle : 0.582 7.772 14811 Z= 0.292 Chirality : 0.039 0.137 1768 Planarity : 0.004 0.045 1846 Dihedral : 3.714 21.531 1476 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.41 % Allowed : 16.26 % Favored : 80.32 % 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: 1.53 (0.24), residues: 1316 helix: 2.32 (0.18), residues: 820 sheet: -0.88 (0.54), residues: 82 loop : -1.34 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 380 HIS 0.003 0.001 HIS C 72 PHE 0.011 0.001 PHE D 547 TYR 0.021 0.002 TYR F 190 ARG 0.002 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 56 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9059 (mmm) cc_final: 0.8792 (mmm) REVERT: A 290 ASN cc_start: 0.9182 (m-40) cc_final: 0.8777 (p0) REVERT: B 72 HIS cc_start: 0.8715 (OUTLIER) cc_final: 0.8057 (m170) REVERT: D 102 LEU cc_start: 0.9008 (mm) cc_final: 0.8613 (mm) REVERT: D 490 MET cc_start: 0.8324 (ppp) cc_final: 0.8059 (ppp) REVERT: D 603 ASP cc_start: 0.7430 (t0) cc_final: 0.7203 (t0) REVERT: D 608 MET cc_start: 0.8369 (ptt) cc_final: 0.7789 (ppp) REVERT: E 81 MET cc_start: 0.8831 (ttm) cc_final: 0.8269 (tmm) outliers start: 38 outliers final: 27 residues processed: 90 average time/residue: 0.1665 time to fit residues: 24.7632 Evaluate side-chains 78 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 50 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10918 Z= 0.256 Angle : 0.554 7.432 14811 Z= 0.275 Chirality : 0.038 0.137 1768 Planarity : 0.003 0.051 1846 Dihedral : 3.654 21.687 1476 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.32 % Allowed : 17.88 % Favored : 78.80 % 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: 1.76 (0.24), residues: 1316 helix: 2.45 (0.18), residues: 824 sheet: -0.55 (0.56), residues: 82 loop : -1.23 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 380 HIS 0.003 0.001 HIS C 72 PHE 0.009 0.001 PHE D 547 TYR 0.019 0.001 TYR F 190 ARG 0.002 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 54 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7751 (tp40) REVERT: A 237 TYR cc_start: 0.6290 (OUTLIER) cc_final: 0.5579 (m-10) REVERT: A 249 MET cc_start: 0.9053 (mmm) cc_final: 0.8783 (mmm) REVERT: A 290 ASN cc_start: 0.9256 (m-40) cc_final: 0.8764 (p0) REVERT: B 72 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.7986 (m170) REVERT: D 102 LEU cc_start: 0.9004 (mm) cc_final: 0.8605 (mm) REVERT: D 490 MET cc_start: 0.8276 (ppp) cc_final: 0.8026 (ppp) REVERT: D 526 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8355 (pp) REVERT: D 603 ASP cc_start: 0.7457 (t0) cc_final: 0.7245 (t0) REVERT: D 608 MET cc_start: 0.8294 (ptt) cc_final: 0.7725 (ppp) REVERT: E 81 MET cc_start: 0.8824 (ttm) cc_final: 0.8252 (tmm) outliers start: 37 outliers final: 25 residues processed: 87 average time/residue: 0.1621 time to fit residues: 23.1613 Evaluate side-chains 78 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 49 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10918 Z= 0.288 Angle : 0.580 7.663 14811 Z= 0.288 Chirality : 0.039 0.138 1768 Planarity : 0.003 0.048 1846 Dihedral : 3.688 21.623 1476 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.86 % Allowed : 18.33 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1316 helix: 2.42 (0.18), residues: 824 sheet: -0.50 (0.60), residues: 72 loop : -1.16 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 380 HIS 0.003 0.001 HIS C 72 PHE 0.010 0.001 PHE D 547 TYR 0.021 0.002 TYR F 190 ARG 0.003 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 53 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 237 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.5798 (m-10) REVERT: A 249 MET cc_start: 0.9055 (mmm) cc_final: 0.8799 (mmm) REVERT: A 290 ASN cc_start: 0.9244 (m-40) cc_final: 0.8771 (p0) REVERT: B 72 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.8067 (m170) REVERT: D 102 LEU cc_start: 0.9016 (mm) cc_final: 0.8625 (mm) REVERT: D 490 MET cc_start: 0.8307 (ppp) cc_final: 0.7862 (ppp) REVERT: D 526 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8373 (pp) REVERT: D 608 MET cc_start: 0.8226 (ptt) cc_final: 0.7701 (ppp) REVERT: E 81 MET cc_start: 0.8839 (ttm) cc_final: 0.8260 (tmm) outliers start: 43 outliers final: 32 residues processed: 91 average time/residue: 0.1635 time to fit residues: 24.7101 Evaluate side-chains 84 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 49 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 82 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10918 Z= 0.231 Angle : 0.545 7.383 14811 Z= 0.272 Chirality : 0.038 0.137 1768 Planarity : 0.003 0.048 1846 Dihedral : 3.599 21.391 1476 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.14 % Allowed : 19.68 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1316 helix: 2.55 (0.19), residues: 824 sheet: -0.34 (0.61), residues: 72 loop : -1.11 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 380 HIS 0.003 0.001 HIS D 309 PHE 0.009 0.001 PHE D 547 TYR 0.019 0.001 TYR F 190 ARG 0.003 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 55 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 118 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7721 (tp40) REVERT: A 237 TYR cc_start: 0.6356 (OUTLIER) cc_final: 0.5823 (m-10) REVERT: A 249 MET cc_start: 0.9049 (mmm) cc_final: 0.8781 (mmm) REVERT: A 290 ASN cc_start: 0.9247 (m-40) cc_final: 0.8767 (p0) REVERT: B 72 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.8045 (m170) REVERT: D 102 LEU cc_start: 0.9015 (mm) cc_final: 0.8646 (mm) REVERT: D 490 MET cc_start: 0.8281 (ppp) cc_final: 0.8016 (ppp) REVERT: D 526 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8337 (pp) REVERT: D 608 MET cc_start: 0.8192 (ptt) cc_final: 0.7689 (ppp) REVERT: E 81 MET cc_start: 0.8828 (ttm) cc_final: 0.8253 (tmm) outliers start: 35 outliers final: 28 residues processed: 86 average time/residue: 0.1541 time to fit residues: 21.8854 Evaluate side-chains 83 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 51 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN D 334 HIS E 174 GLN F 30 GLN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10918 Z= 0.185 Angle : 0.530 9.625 14811 Z= 0.261 Chirality : 0.038 0.134 1768 Planarity : 0.003 0.047 1846 Dihedral : 3.508 20.978 1476 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.41 % Allowed : 19.50 % Favored : 77.09 % 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: 2.05 (0.25), residues: 1316 helix: 2.63 (0.19), residues: 825 sheet: -0.21 (0.61), residues: 72 loop : -1.05 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 14 HIS 0.003 0.001 HIS D 309 PHE 0.010 0.001 PHE B 64 TYR 0.018 0.001 TYR F 190 ARG 0.002 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 59 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 118 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7825 (tp40) REVERT: A 237 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.5796 (m-10) REVERT: A 249 MET cc_start: 0.9021 (mmm) cc_final: 0.8729 (mmm) REVERT: A 290 ASN cc_start: 0.9227 (m-40) cc_final: 0.8758 (p0) REVERT: B 72 HIS cc_start: 0.8713 (OUTLIER) cc_final: 0.8054 (m170) REVERT: D 102 LEU cc_start: 0.9019 (mm) cc_final: 0.8648 (mm) REVERT: D 490 MET cc_start: 0.8273 (ppp) cc_final: 0.8008 (ppp) REVERT: D 526 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8391 (pp) REVERT: D 608 MET cc_start: 0.8134 (ptt) cc_final: 0.7635 (ppp) REVERT: E 81 MET cc_start: 0.8820 (ttm) cc_final: 0.8238 (tmm) outliers start: 38 outliers final: 27 residues processed: 93 average time/residue: 0.1578 time to fit residues: 24.3050 Evaluate side-chains 82 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 51 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 126 optimal weight: 0.0060 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 HIS ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10918 Z= 0.152 Angle : 0.530 11.379 14811 Z= 0.257 Chirality : 0.037 0.159 1768 Planarity : 0.003 0.047 1846 Dihedral : 3.383 20.379 1476 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.16 % Allowed : 21.11 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.25), residues: 1316 helix: 2.68 (0.18), residues: 825 sheet: -0.05 (0.61), residues: 72 loop : -0.94 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 14 HIS 0.004 0.001 HIS D 309 PHE 0.007 0.001 PHE A 92 TYR 0.017 0.001 TYR F 190 ARG 0.002 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 58 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9338 (tt) cc_final: 0.9057 (tp) REVERT: A 237 TYR cc_start: 0.6279 (OUTLIER) cc_final: 0.5801 (m-10) REVERT: A 249 MET cc_start: 0.8997 (mmm) cc_final: 0.8700 (mmm) REVERT: A 290 ASN cc_start: 0.9188 (m-40) cc_final: 0.8726 (p0) REVERT: B 72 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8021 (m170) REVERT: D 102 LEU cc_start: 0.8991 (mm) cc_final: 0.8614 (mm) REVERT: D 490 MET cc_start: 0.8212 (ppp) cc_final: 0.7978 (ppp) REVERT: D 526 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8398 (pp) REVERT: D 608 MET cc_start: 0.8127 (ptt) cc_final: 0.7648 (ppp) REVERT: E 81 MET cc_start: 0.8801 (ttm) cc_final: 0.8220 (tmm) outliers start: 24 outliers final: 18 residues processed: 79 average time/residue: 0.1705 time to fit residues: 22.2945 Evaluate side-chains 75 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 54 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 165 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 136 optimal weight: 50.0000 chunk 125 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 282 HIS D 334 HIS ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10918 Z= 0.151 Angle : 0.527 12.009 14811 Z= 0.254 Chirality : 0.037 0.157 1768 Planarity : 0.003 0.046 1846 Dihedral : 3.258 19.493 1476 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.25 % Allowed : 21.11 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.25), residues: 1316 helix: 2.73 (0.19), residues: 825 sheet: 0.13 (0.61), residues: 72 loop : -0.85 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 14 HIS 0.004 0.001 HIS D 309 PHE 0.008 0.001 PHE A 114 TYR 0.016 0.001 TYR F 190 ARG 0.002 0.000 ARG A 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 57 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 237 TYR cc_start: 0.6192 (OUTLIER) cc_final: 0.5730 (m-10) REVERT: A 249 MET cc_start: 0.9003 (mmm) cc_final: 0.8674 (mmm) REVERT: A 290 ASN cc_start: 0.9183 (m-40) cc_final: 0.8734 (p0) REVERT: C 48 THR cc_start: 0.8829 (m) cc_final: 0.8603 (p) REVERT: B 72 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.7921 (m170) REVERT: D 102 LEU cc_start: 0.9027 (mm) cc_final: 0.8672 (mm) REVERT: D 490 MET cc_start: 0.8238 (ppp) cc_final: 0.7976 (ppp) REVERT: D 526 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8404 (pp) REVERT: D 608 MET cc_start: 0.8281 (ptt) cc_final: 0.7713 (ppp) REVERT: E 81 MET cc_start: 0.8832 (ttm) cc_final: 0.8350 (tmm) outliers start: 25 outliers final: 19 residues processed: 79 average time/residue: 0.1627 time to fit residues: 21.4066 Evaluate side-chains 77 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 55 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 165 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 95 optimal weight: 0.1980 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN D 334 HIS ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 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 = 0.3292 r_free = 0.3292 target = 0.058868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.043474 restraints weight = 59014.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.044672 restraints weight = 33055.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.045443 restraints weight = 22920.263| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10918 Z= 0.253 Angle : 0.604 13.575 14811 Z= 0.290 Chirality : 0.039 0.191 1768 Planarity : 0.003 0.044 1846 Dihedral : 3.430 20.064 1476 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.34 % Allowed : 21.29 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.25), residues: 1316 helix: 2.65 (0.19), residues: 825 sheet: -0.01 (0.61), residues: 72 loop : -0.88 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 14 HIS 0.003 0.001 HIS C 72 PHE 0.010 0.001 PHE D 547 TYR 0.021 0.001 TYR F 190 ARG 0.003 0.000 ARG F 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.25 seconds wall clock time: 33 minutes 7.51 seconds (1987.51 seconds total)