Starting phenix.real_space_refine on Fri Feb 14 19:45:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kas_22782/02_2025/7kas_22782.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kas_22782/02_2025/7kas_22782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kas_22782/02_2025/7kas_22782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kas_22782/02_2025/7kas_22782.map" model { file = "/net/cci-nas-00/data/ceres_data/7kas_22782/02_2025/7kas_22782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kas_22782/02_2025/7kas_22782.cif" } resolution = 3.9 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= 0.003 sd= 0.052 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 41 5.16 5 C 6915 2.51 5 N 1791 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10616 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3268 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 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: 3804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3804 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 27, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 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: 6.36, per 1000 atoms: 0.60 Number of scatterers: 10616 At special positions: 0 Unit cell: (110.67, 126.14, 135.66, 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 41 16.00 O 1869 8.00 N 1791 7.00 C 6915 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: 2.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 70.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.564A pdb=" N LYS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.577A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 4.106A 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 214 through 224 Processing helix chain 'A' and resid 227 through 237 removed outlier: 4.130A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.858A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.563A pdb=" N MET A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.574A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 384 removed outlier: 3.604A pdb=" N THR A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 417 through 440 Processing helix chain 'A' and resid 444 through 466 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.991A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 3.548A 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: 3.863A 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: 4.484A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 94 through 112 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 219 through 233 removed outlier: 4.103A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.678A pdb=" N SER D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.592A pdb=" N ALA D 259 " --> pdb=" O HIS D 255 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.913A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.651A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.795A 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: 4.131A 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: 5.629A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 362 Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.571A 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: 3.988A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.220A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 480 through 486 removed outlier: 3.593A pdb=" N ASP D 486 " --> pdb=" O GLU D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 4.311A pdb=" N MET D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 541 removed outlier: 4.493A pdb=" N ASN D 539 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.789A pdb=" N TYR E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 124 removed outlier: 4.155A pdb=" N LEU E 92 " --> pdb=" O HIS E 88 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.642A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 182 removed outlier: 4.041A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.793A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.640A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.699A 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: 3.564A pdb=" N GLU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.989A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 removed outlier: 3.874A pdb=" N LYS F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 120 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: 4.008A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 174 through 192 removed outlier: 3.923A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 170 Processing helix chain 'G' and resid 175 through 205 removed outlier: 3.573A pdb=" N UNK G 205 " --> pdb=" O UNK G 201 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211 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 450 through 453 removed outlier: 3.662A pdb=" N ILE D 571 " --> pdb=" O LEU D 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.522A pdb=" N ILE D 604 " --> pdb=" O VAL D 590 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.804A pdb=" N GLY D 584 " --> pdb=" O VAL D 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 6 689 hydrogen bonds defined for protein. 2025 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: 3.06 Time building geometry restraints manager: 3.42 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: 3355 1.34 - 1.46: 1582 1.46 - 1.57: 5818 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 10820 Sorted by residual: bond pdb=" C THR D 595 " pdb=" N ASP D 596 " ideal model delta sigma weight residual 1.333 1.317 0.016 1.41e-02 5.03e+03 1.36e+00 bond pdb=" CB TRP D 283 " pdb=" CG TRP D 283 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.27e+00 bond pdb=" CB TRP D 513 " pdb=" CG TRP D 513 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 1.01e+00 bond pdb=" CA VAL A 27 " pdb=" CB VAL A 27 " ideal model delta sigma weight residual 1.537 1.525 0.013 1.29e-02 6.01e+03 9.62e-01 bond pdb=" N LEU F 102 " pdb=" CA LEU F 102 " ideal model delta sigma weight residual 1.463 1.457 0.007 6.90e-03 2.10e+04 8.92e-01 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 14226 1.49 - 2.98: 375 2.98 - 4.47: 52 4.47 - 5.96: 19 5.96 - 7.45: 4 Bond angle restraints: 14676 Sorted by residual: angle pdb=" N VAL E 205 " pdb=" CA VAL E 205 " pdb=" C VAL E 205 " ideal model delta sigma weight residual 111.88 106.81 5.07 1.06e+00 8.90e-01 2.28e+01 angle pdb=" N VAL D 25 " pdb=" CA VAL D 25 " pdb=" C VAL D 25 " ideal model delta sigma weight residual 111.90 108.73 3.17 8.10e-01 1.52e+00 1.54e+01 angle pdb=" C GLU D 12 " pdb=" N THR D 13 " pdb=" CA THR D 13 " ideal model delta sigma weight residual 122.08 117.55 4.53 1.53e+00 4.27e-01 8.76e+00 angle pdb=" N PRO D 426 " pdb=" CA PRO D 426 " pdb=" C PRO D 426 " ideal model delta sigma weight residual 110.21 114.91 -4.70 1.64e+00 3.72e-01 8.21e+00 angle pdb=" C THR D 595 " pdb=" N ASP D 596 " pdb=" CA ASP D 596 " ideal model delta sigma weight residual 121.52 117.30 4.22 1.74e+00 3.30e-01 5.89e+00 ... (remaining 14671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5908 17.76 - 35.51: 506 35.51 - 53.27: 80 53.27 - 71.03: 14 71.03 - 88.78: 7 Dihedral angle restraints: 6515 sinusoidal: 2489 harmonic: 4026 Sorted by residual: dihedral pdb=" CA ARG F 154 " pdb=" C ARG F 154 " pdb=" N GLN F 155 " pdb=" CA GLN F 155 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA LEU F 153 " pdb=" C LEU F 153 " pdb=" N ARG F 154 " pdb=" CA ARG F 154 " ideal model delta harmonic sigma weight residual 180.00 162.92 17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ARG D 509 " pdb=" C ARG D 509 " pdb=" N ARG D 510 " pdb=" CA ARG D 510 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 6512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 986 0.028 - 0.056: 507 0.056 - 0.084: 160 0.084 - 0.112: 77 0.112 - 0.140: 21 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CB ILE E 170 " pdb=" CA ILE E 170 " pdb=" CG1 ILE E 170 " pdb=" CG2 ILE E 170 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CB VAL E 205 " pdb=" CA VAL E 205 " pdb=" CG1 VAL E 205 " pdb=" CG2 VAL E 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.48e-01 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 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1748 not shown) Planarity restraints: 1831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 53 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 54 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 366 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO D 367 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " 0.020 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 3.50e-02 1.96e+00 pdb=" N PRO F 94 " 0.061 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 ... (remaining 1828 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 299 2.71 - 3.26: 11030 3.26 - 3.80: 16319 3.80 - 4.35: 18560 4.35 - 4.90: 32083 Nonbonded interactions: 78291 Sorted by model distance: nonbonded pdb=" OE1 GLN D 370 " pdb=" OG1 THR D 391 " model vdw 2.162 3.040 nonbonded pdb=" ND2 ASN D 55 " pdb=" O LEU D 496 " model vdw 2.250 3.120 nonbonded pdb=" O TYR A 237 " pdb=" ND2 ASN A 243 " model vdw 2.269 3.120 nonbonded pdb=" O SER D 423 " pdb=" OG SER D 423 " model vdw 2.293 3.040 nonbonded pdb=" O PRO F 171 " pdb=" NH2 ARG F 177 " model vdw 2.293 3.120 ... (remaining 78286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10820 Z= 0.246 Angle : 0.619 7.450 14676 Z= 0.349 Chirality : 0.040 0.140 1751 Planarity : 0.004 0.037 1831 Dihedral : 13.683 88.782 3899 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.22), residues: 1305 helix: 0.09 (0.17), residues: 809 sheet: -2.52 (0.51), residues: 84 loop : -2.44 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 14 HIS 0.006 0.001 HIS B 72 PHE 0.010 0.001 PHE F 46 TYR 0.021 0.001 TYR F 190 ARG 0.003 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 24 MET cc_start: 0.8717 (mmm) cc_final: 0.8412 (tpp) REVERT: E 73 ASP cc_start: 0.8497 (p0) cc_final: 0.8200 (p0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2654 time to fit residues: 44.8461 Evaluate side-chains 64 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 427 ASN D 539 ASN D 558 HIS E 88 HIS F 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.083352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.061246 restraints weight = 46064.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062944 restraints weight = 24879.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.064037 restraints weight = 17288.280| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10820 Z= 0.222 Angle : 0.572 9.526 14676 Z= 0.290 Chirality : 0.039 0.161 1751 Planarity : 0.004 0.034 1831 Dihedral : 3.730 18.959 1463 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.36 % Allowed : 12.96 % Favored : 85.68 % 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: 0.21 (0.24), residues: 1305 helix: 1.43 (0.18), residues: 819 sheet: -2.38 (0.48), residues: 94 loop : -2.00 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 195 HIS 0.005 0.001 HIS D 309 PHE 0.016 0.001 PHE A 256 TYR 0.016 0.001 TYR E 121 ARG 0.004 0.000 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 CYS cc_start: 0.9348 (m) cc_final: 0.9113 (p) REVERT: B 64 PHE cc_start: 0.9195 (t80) cc_final: 0.8927 (t80) REVERT: D 24 MET cc_start: 0.8998 (mmm) cc_final: 0.8724 (tpp) REVERT: E 165 MET cc_start: 0.8211 (ttp) cc_final: 0.7469 (tmm) outliers start: 15 outliers final: 11 residues processed: 87 average time/residue: 0.2035 time to fit residues: 27.2512 Evaluate side-chains 81 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 606 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 43 optimal weight: 10.0000 chunk 76 optimal weight: 0.0970 chunk 65 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.086107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065013 restraints weight = 46170.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065622 restraints weight = 26586.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.066242 restraints weight = 18389.773| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10820 Z= 0.162 Angle : 0.522 9.443 14676 Z= 0.259 Chirality : 0.038 0.143 1751 Planarity : 0.004 0.039 1831 Dihedral : 3.485 17.734 1463 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.99 % Allowed : 15.23 % Favored : 82.77 % 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: 1.01 (0.24), residues: 1305 helix: 2.03 (0.19), residues: 816 sheet: -1.95 (0.49), residues: 94 loop : -1.63 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 95 HIS 0.006 0.001 HIS D 309 PHE 0.015 0.001 PHE A 256 TYR 0.013 0.001 TYR E 121 ARG 0.002 0.000 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8312 (tpt) cc_final: 0.7953 (tpt) REVERT: A 256 PHE cc_start: 0.8983 (t80) cc_final: 0.8596 (t80) REVERT: B 64 PHE cc_start: 0.9002 (t80) cc_final: 0.8505 (t80) REVERT: D 24 MET cc_start: 0.9022 (mmm) cc_final: 0.8631 (tpp) REVERT: D 440 ARG cc_start: 0.7474 (mmm160) cc_final: 0.7188 (mmm160) REVERT: E 165 MET cc_start: 0.8251 (ttp) cc_final: 0.7733 (tmm) REVERT: F 87 MET cc_start: 0.8591 (tpp) cc_final: 0.8390 (tpp) outliers start: 22 outliers final: 17 residues processed: 102 average time/residue: 0.1895 time to fit residues: 30.2254 Evaluate side-chains 80 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 186 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 132 optimal weight: 40.0000 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 HIS E 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.082250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.060453 restraints weight = 46155.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.061597 restraints weight = 27572.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.062233 restraints weight = 18015.709| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10820 Z= 0.333 Angle : 0.626 10.887 14676 Z= 0.315 Chirality : 0.041 0.155 1751 Planarity : 0.004 0.034 1831 Dihedral : 3.824 18.039 1463 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.72 % Allowed : 16.95 % Favored : 79.33 % 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: 0.97 (0.24), residues: 1305 helix: 1.98 (0.18), residues: 815 sheet: -1.82 (0.51), residues: 94 loop : -1.63 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 95 HIS 0.004 0.001 HIS F 122 PHE 0.020 0.002 PHE D 356 TYR 0.023 0.002 TYR F 190 ARG 0.005 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8044 (tpt) cc_final: 0.7631 (tpt) REVERT: A 194 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8847 (m-80) REVERT: A 256 PHE cc_start: 0.8946 (t80) cc_final: 0.8589 (t80) REVERT: A 373 CYS cc_start: 0.9296 (m) cc_final: 0.9079 (p) REVERT: B 64 PHE cc_start: 0.9171 (t80) cc_final: 0.8879 (t80) REVERT: D 24 MET cc_start: 0.9085 (mmm) cc_final: 0.8662 (tpp) REVERT: D 490 MET cc_start: 0.9030 (ppp) cc_final: 0.8724 (ppp) REVERT: D 526 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.7984 (pp) REVERT: E 98 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8619 (m-40) REVERT: E 165 MET cc_start: 0.8311 (ttp) cc_final: 0.8019 (tmm) REVERT: F 87 MET cc_start: 0.8653 (tpp) cc_final: 0.8432 (tpp) REVERT: F 186 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8467 (t0) outliers start: 41 outliers final: 23 residues processed: 99 average time/residue: 0.1874 time to fit residues: 29.1432 Evaluate side-chains 87 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 310 ILE 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 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 186 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 127 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 87 optimal weight: 0.3980 chunk 123 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.083213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061091 restraints weight = 46392.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062655 restraints weight = 28008.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.064143 restraints weight = 18432.106| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10820 Z= 0.218 Angle : 0.566 10.293 14676 Z= 0.281 Chirality : 0.039 0.207 1751 Planarity : 0.004 0.035 1831 Dihedral : 3.649 17.561 1463 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.17 % Allowed : 19.22 % Favored : 77.61 % 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: 1.29 (0.25), residues: 1305 helix: 2.21 (0.18), residues: 811 sheet: -1.60 (0.53), residues: 94 loop : -1.42 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 95 HIS 0.005 0.001 HIS D 309 PHE 0.014 0.001 PHE A 92 TYR 0.018 0.001 TYR F 190 ARG 0.006 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7987 (tpt) cc_final: 0.7611 (tpt) REVERT: A 256 PHE cc_start: 0.9003 (t80) cc_final: 0.8634 (t80) REVERT: A 400 MET cc_start: 0.9249 (mmm) cc_final: 0.8998 (mmm) REVERT: B 64 PHE cc_start: 0.9155 (t80) cc_final: 0.8821 (t80) REVERT: D 24 MET cc_start: 0.9051 (mmm) cc_final: 0.8612 (tpp) REVERT: D 440 ARG cc_start: 0.7315 (mmm160) cc_final: 0.7013 (mmm160) REVERT: D 490 MET cc_start: 0.8943 (ppp) cc_final: 0.8663 (ppp) REVERT: E 147 ASP cc_start: 0.8966 (m-30) cc_final: 0.8724 (p0) REVERT: E 165 MET cc_start: 0.8221 (ttp) cc_final: 0.7887 (tmm) REVERT: F 87 MET cc_start: 0.8654 (tpp) cc_final: 0.8451 (tpp) REVERT: F 186 ASN cc_start: 0.9068 (OUTLIER) cc_final: 0.8477 (t0) outliers start: 35 outliers final: 22 residues processed: 97 average time/residue: 0.1776 time to fit residues: 26.9521 Evaluate side-chains 83 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 186 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 135 optimal weight: 60.0000 chunk 27 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.084170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062269 restraints weight = 46576.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.063991 restraints weight = 25253.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.065034 restraints weight = 17609.684| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10820 Z= 0.160 Angle : 0.532 10.805 14676 Z= 0.264 Chirality : 0.039 0.251 1751 Planarity : 0.003 0.034 1831 Dihedral : 3.465 17.136 1463 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.18 % Allowed : 20.85 % Favored : 76.97 % 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: 1.49 (0.25), residues: 1305 helix: 2.27 (0.18), residues: 819 sheet: -1.30 (0.55), residues: 94 loop : -1.26 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 95 HIS 0.006 0.001 HIS D 309 PHE 0.022 0.001 PHE A 395 TYR 0.014 0.001 TYR F 190 ARG 0.002 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7985 (tpt) cc_final: 0.7617 (tpt) REVERT: A 256 PHE cc_start: 0.8902 (t80) cc_final: 0.8531 (t80) REVERT: A 373 CYS cc_start: 0.9185 (m) cc_final: 0.8979 (p) REVERT: B 64 PHE cc_start: 0.9015 (t80) cc_final: 0.8426 (t80) REVERT: D 24 MET cc_start: 0.9077 (mmm) cc_final: 0.8713 (tpp) REVERT: D 440 ARG cc_start: 0.7260 (mmm160) cc_final: 0.6952 (mmm160) REVERT: D 490 MET cc_start: 0.8781 (ppp) cc_final: 0.8471 (ppp) REVERT: D 526 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.7784 (pp) REVERT: E 165 MET cc_start: 0.8119 (ttp) cc_final: 0.7732 (tmm) REVERT: F 87 MET cc_start: 0.8477 (tpp) cc_final: 0.8271 (tpp) REVERT: F 186 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.8460 (t0) outliers start: 24 outliers final: 17 residues processed: 87 average time/residue: 0.1844 time to fit residues: 25.5673 Evaluate side-chains 83 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 186 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 7 optimal weight: 0.0470 chunk 103 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 132 optimal weight: 40.0000 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 135 optimal weight: 60.0000 overall best weight: 1.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.083401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.062687 restraints weight = 46687.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.063925 restraints weight = 26011.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.064538 restraints weight = 17136.759| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10820 Z= 0.179 Angle : 0.558 10.773 14676 Z= 0.272 Chirality : 0.039 0.237 1751 Planarity : 0.003 0.034 1831 Dihedral : 3.425 17.010 1463 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.81 % Allowed : 20.40 % Favored : 76.79 % 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: 1.58 (0.25), residues: 1305 helix: 2.30 (0.18), residues: 814 sheet: -1.19 (0.56), residues: 94 loop : -1.08 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 95 HIS 0.006 0.001 HIS D 309 PHE 0.017 0.001 PHE C 28 TYR 0.016 0.001 TYR F 190 ARG 0.002 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7970 (tpt) cc_final: 0.7595 (tpt) REVERT: A 256 PHE cc_start: 0.8956 (t80) cc_final: 0.8569 (t80) REVERT: B 64 PHE cc_start: 0.9045 (t80) cc_final: 0.8474 (t80) REVERT: D 24 MET cc_start: 0.9067 (mmm) cc_final: 0.8685 (tpp) REVERT: D 440 ARG cc_start: 0.7498 (mmm160) cc_final: 0.7222 (mmm160) REVERT: D 490 MET cc_start: 0.9004 (ppp) cc_final: 0.8688 (ppp) REVERT: D 526 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.7775 (pp) REVERT: E 165 MET cc_start: 0.8205 (ttp) cc_final: 0.7773 (tmm) REVERT: F 186 ASN cc_start: 0.9096 (OUTLIER) cc_final: 0.8464 (t0) outliers start: 31 outliers final: 22 residues processed: 93 average time/residue: 0.1823 time to fit residues: 26.9345 Evaluate side-chains 88 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 186 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 135 optimal weight: 60.0000 chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 84 optimal weight: 0.0980 chunk 27 optimal weight: 8.9990 chunk 132 optimal weight: 50.0000 chunk 128 optimal weight: 5.9990 chunk 122 optimal weight: 0.3980 chunk 71 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.083829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.064213 restraints weight = 46108.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.064632 restraints weight = 26872.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.065744 restraints weight = 18008.362| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10820 Z= 0.162 Angle : 0.545 11.115 14676 Z= 0.269 Chirality : 0.039 0.229 1751 Planarity : 0.003 0.035 1831 Dihedral : 3.343 16.723 1463 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.18 % Allowed : 21.58 % Favored : 76.25 % 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: 1.66 (0.25), residues: 1305 helix: 2.32 (0.18), residues: 819 sheet: -1.04 (0.57), residues: 94 loop : -1.04 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 159 HIS 0.006 0.001 HIS D 309 PHE 0.017 0.001 PHE C 28 TYR 0.015 0.001 TYR F 190 ARG 0.002 0.000 ARG E 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7946 (tpt) cc_final: 0.7550 (tpt) REVERT: A 256 PHE cc_start: 0.8934 (t80) cc_final: 0.8555 (t80) REVERT: B 64 PHE cc_start: 0.9003 (t80) cc_final: 0.8396 (t80) REVERT: D 24 MET cc_start: 0.9050 (mmm) cc_final: 0.8696 (tpp) REVERT: D 440 ARG cc_start: 0.7432 (mmm160) cc_final: 0.7137 (mmm160) REVERT: D 490 MET cc_start: 0.8963 (ppp) cc_final: 0.8651 (ppp) REVERT: D 491 MET cc_start: 0.8853 (ttp) cc_final: 0.8437 (ttp) REVERT: D 526 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.7827 (pp) REVERT: E 165 MET cc_start: 0.8166 (ttp) cc_final: 0.7711 (tmm) REVERT: F 186 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8441 (t0) outliers start: 24 outliers final: 20 residues processed: 87 average time/residue: 0.1686 time to fit residues: 23.6305 Evaluate side-chains 86 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 425 ILE 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 F residue 162 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 186 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.084780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063649 restraints weight = 46622.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.065317 restraints weight = 25691.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.066378 restraints weight = 17962.107| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10820 Z= 0.144 Angle : 0.544 11.350 14676 Z= 0.263 Chirality : 0.038 0.222 1751 Planarity : 0.003 0.036 1831 Dihedral : 3.268 16.565 1463 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.36 % Allowed : 21.67 % Favored : 75.97 % 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: 1.72 (0.25), residues: 1305 helix: 2.34 (0.18), residues: 821 sheet: -0.98 (0.56), residues: 94 loop : -0.96 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 159 HIS 0.006 0.001 HIS D 309 PHE 0.016 0.001 PHE C 28 TYR 0.014 0.001 TYR F 190 ARG 0.001 0.000 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8018 (tpt) cc_final: 0.7642 (tpt) REVERT: A 256 PHE cc_start: 0.8975 (t80) cc_final: 0.8623 (t80) REVERT: A 260 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9174 (tp) REVERT: B 64 PHE cc_start: 0.9003 (t80) cc_final: 0.8362 (t80) REVERT: D 24 MET cc_start: 0.9048 (mmm) cc_final: 0.8755 (tpp) REVERT: D 440 ARG cc_start: 0.7301 (mmm160) cc_final: 0.6801 (mmm160) REVERT: D 490 MET cc_start: 0.8870 (ppp) cc_final: 0.8502 (ppp) REVERT: D 491 MET cc_start: 0.8876 (ttp) cc_final: 0.8467 (ttp) REVERT: D 526 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.7813 (pp) REVERT: E 165 MET cc_start: 0.8109 (ttp) cc_final: 0.7715 (tmm) outliers start: 26 outliers final: 20 residues processed: 88 average time/residue: 0.1723 time to fit residues: 24.3958 Evaluate side-chains 84 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 40.0000 chunk 128 optimal weight: 0.0170 chunk 7 optimal weight: 0.0370 chunk 72 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.085582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064326 restraints weight = 47425.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.066008 restraints weight = 25995.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066928 restraints weight = 18218.884| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10820 Z= 0.139 Angle : 0.551 11.253 14676 Z= 0.270 Chirality : 0.038 0.218 1751 Planarity : 0.004 0.067 1831 Dihedral : 3.214 16.233 1463 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.36 % Allowed : 22.76 % Favored : 75.88 % 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: 1.80 (0.25), residues: 1305 helix: 2.36 (0.19), residues: 822 sheet: -0.91 (0.56), residues: 94 loop : -0.84 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 159 HIS 0.007 0.001 HIS D 309 PHE 0.016 0.001 PHE C 28 TYR 0.012 0.001 TYR E 121 ARG 0.002 0.000 ARG F 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9080 (tp) cc_final: 0.8875 (tt) REVERT: A 90 MET cc_start: 0.7953 (tpt) cc_final: 0.7555 (tpt) REVERT: A 256 PHE cc_start: 0.8934 (t80) cc_final: 0.8559 (t80) REVERT: B 64 PHE cc_start: 0.8908 (t80) cc_final: 0.8199 (t80) REVERT: D 24 MET cc_start: 0.8987 (mmm) cc_final: 0.8732 (tpp) REVERT: D 440 ARG cc_start: 0.7380 (mmm160) cc_final: 0.6813 (mmm160) REVERT: D 490 MET cc_start: 0.8836 (ppp) cc_final: 0.8561 (ppp) REVERT: D 491 MET cc_start: 0.8760 (ttp) cc_final: 0.8387 (ttp) REVERT: D 526 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.7792 (pp) REVERT: E 165 MET cc_start: 0.8036 (ttp) cc_final: 0.7530 (tmm) REVERT: F 128 ASP cc_start: 0.8671 (m-30) cc_final: 0.8395 (t0) outliers start: 15 outliers final: 14 residues processed: 86 average time/residue: 0.1978 time to fit residues: 26.3891 Evaluate side-chains 81 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 92 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 77 optimal weight: 5.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.084639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.064350 restraints weight = 46557.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.065455 restraints weight = 26277.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.066187 restraints weight = 17384.221| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10820 Z= 0.153 Angle : 0.578 12.756 14676 Z= 0.276 Chirality : 0.038 0.217 1751 Planarity : 0.003 0.038 1831 Dihedral : 3.200 15.681 1463 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.72 % Allowed : 22.94 % Favored : 75.34 % 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: 1.88 (0.25), residues: 1305 helix: 2.40 (0.18), residues: 817 sheet: -0.91 (0.56), residues: 94 loop : -0.70 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 159 HIS 0.005 0.001 HIS D 309 PHE 0.015 0.001 PHE C 28 TYR 0.015 0.001 TYR F 190 ARG 0.003 0.000 ARG F 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2886.68 seconds wall clock time: 52 minutes 56.11 seconds (3176.11 seconds total)