Starting phenix.real_space_refine on Sat Feb 15 00:10:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kaq_22780/02_2025/7kaq_22780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kaq_22780/02_2025/7kaq_22780.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/cci-nas-00/data/ceres_data/7kaq_22780/02_2025/7kaq_22780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kaq_22780/02_2025/7kaq_22780.map" model { file = "/net/cci-nas-00/data/ceres_data/7kaq_22780/02_2025/7kaq_22780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kaq_22780/02_2025/7kaq_22780.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.064 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 7008 2.51 5 N 1812 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10753 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3345 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 75 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': 3} Unresolved non-hydrogen planarities: 69 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: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3864 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 28, 'TRANS': 463} 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: 6.66, per 1000 atoms: 0.62 Number of scatterers: 10753 At special positions: 0 Unit cell: (108.1, 125.35, 135.7, 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 1894 8.00 N 1812 7.00 C 7008 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: 2.62 Conformation dependent library (CDL) restraints added in 1.4 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2650 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 6 sheets defined 71.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.651A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.838A 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 225 Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.946A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.560A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.722A pdb=" N ILE 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 Processing helix chain 'A' and resid 358 through 384 removed outlier: 3.696A 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 416 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 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.576A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'B' and resid 53 through 82 Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.588A 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 65 removed outlier: 4.239A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (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: 3.777A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.645A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.855A pdb=" N LYS D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 4.325A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.756A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.066A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 removed outlier: 3.517A pdb=" N LEU D 395 " --> pdb=" O THR D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.606A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.079A 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: 4.248A pdb=" N ASP D 486 " --> pdb=" O GLU D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 494 removed outlier: 3.590A pdb=" N LYS D 493 " --> pdb=" O MET D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 545 removed outlier: 6.777A pdb=" N ASP D 542 " --> pdb=" O ASN D 539 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP D 543 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 544 " --> pdb=" O ASN D 541 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP D 545 " --> pdb=" O ASP D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 558 removed outlier: 3.534A pdb=" N HIS D 558 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.595A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 123 Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 3.513A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 182 removed outlier: 3.513A pdb=" N VAL E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.123A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.589A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 41 Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.808A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 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: 3.631A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 4.236A 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: 3.619A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 170 removed outlier: 3.640A 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 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 436 removed outlier: 6.805A pdb=" N LYS D 454 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA D 433 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SER D 452 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE D 435 " --> pdb=" O TYR D 450 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR D 450 " --> pdb=" O PHE D 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 705 hydrogen bonds defined for protein. 2070 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: 3.44 Time building geometry restraints manager: 3.03 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: 3404 1.34 - 1.46: 2126 1.46 - 1.57: 5370 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 10961 Sorted by residual: bond pdb=" C LYS D 493 " pdb=" N GLN D 494 " ideal model delta sigma weight residual 1.331 1.305 0.026 2.83e-02 1.25e+03 8.58e-01 bond pdb=" CA LEU F 102 " pdb=" C LEU F 102 " ideal model delta sigma weight residual 1.521 1.529 -0.008 1.14e-02 7.69e+03 5.47e-01 bond pdb=" CA LEU A 147 " pdb=" C LEU A 147 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.10e-02 2.27e+03 5.27e-01 bond pdb=" C GLU D 12 " pdb=" N THR D 13 " ideal model delta sigma weight residual 1.332 1.322 0.010 1.40e-02 5.10e+03 5.27e-01 bond pdb=" CB VAL C 54 " pdb=" CG1 VAL C 54 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.09e-01 ... (remaining 10956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 14726 1.91 - 3.81: 123 3.81 - 5.72: 18 5.72 - 7.63: 5 7.63 - 9.53: 1 Bond angle restraints: 14873 Sorted by residual: angle pdb=" C ILE A 417 " pdb=" N ILE A 418 " pdb=" CA ILE A 418 " ideal model delta sigma weight residual 120.33 122.46 -2.13 8.00e-01 1.56e+00 7.11e+00 angle pdb=" N PRO D 426 " pdb=" CA PRO D 426 " pdb=" C PRO D 426 " ideal model delta sigma weight residual 110.55 114.48 -3.93 1.63e+00 3.76e-01 5.80e+00 angle pdb=" C ILE A 418 " pdb=" CA ILE A 418 " pdb=" CB ILE A 418 " ideal model delta sigma weight residual 114.00 110.93 3.07 1.31e+00 5.83e-01 5.48e+00 angle pdb=" N VAL D 25 " pdb=" CA VAL D 25 " pdb=" C VAL D 25 " ideal model delta sigma weight residual 111.81 109.93 1.88 8.60e-01 1.35e+00 4.79e+00 angle pdb=" C PRO D 471 " pdb=" N GLU D 472 " pdb=" CA GLU D 472 " ideal model delta sigma weight residual 121.54 125.52 -3.98 1.91e+00 2.74e-01 4.35e+00 ... (remaining 14868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6189 17.67 - 35.33: 338 35.33 - 53.00: 54 53.00 - 70.67: 5 70.67 - 88.33: 9 Dihedral angle restraints: 6595 sinusoidal: 2518 harmonic: 4077 Sorted by residual: dihedral pdb=" CA SER A 289 " pdb=" C SER A 289 " pdb=" N ASN A 290 " pdb=" CA ASN A 290 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB GLU E 144 " pdb=" CG GLU E 144 " pdb=" CD GLU E 144 " pdb=" OE1 GLU E 144 " ideal model delta sinusoidal sigma weight residual 0.00 -88.33 88.33 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU F 63 " pdb=" CG GLU F 63 " pdb=" CD GLU F 63 " pdb=" OE1 GLU F 63 " ideal model delta sinusoidal sigma weight residual 0.00 -88.00 88.00 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 6592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1075 0.027 - 0.054: 452 0.054 - 0.080: 160 0.080 - 0.107: 78 0.107 - 0.134: 12 Chirality restraints: 1777 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 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CB THR D 448 " pdb=" CA THR D 448 " pdb=" OG1 THR D 448 " pdb=" CG2 THR D 448 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA SER A 83 " pdb=" N SER A 83 " pdb=" C SER A 83 " pdb=" CB SER A 83 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1774 not shown) Planarity restraints: 1855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO F 48 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 462 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO D 463 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 463 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 463 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 93 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO F 94 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO F 94 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 94 " -0.014 5.00e-02 4.00e+02 ... (remaining 1852 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 287 2.71 - 3.25: 11487 3.25 - 3.80: 17396 3.80 - 4.35: 20289 4.35 - 4.90: 34815 Nonbonded interactions: 84274 Sorted by model distance: nonbonded pdb=" OH TYR A 287 " pdb=" OG1 THR A 386 " model vdw 2.158 3.040 nonbonded pdb=" OG SER A 72 " pdb=" O LEU A 78 " model vdw 2.214 3.040 nonbonded pdb=" NH1 ARG F 92 " pdb=" OE1 GLU F 96 " model vdw 2.242 3.120 nonbonded pdb=" O THR D 444 " pdb=" OG SER D 447 " model vdw 2.247 3.040 nonbonded pdb=" O PHE A 198 " pdb=" OH TYR C 66 " model vdw 2.252 3.040 ... (remaining 84269 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.490 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 0.026 10961 Z= 0.167 Angle : 0.521 9.533 14873 Z= 0.290 Chirality : 0.037 0.134 1777 Planarity : 0.003 0.041 1855 Dihedral : 11.528 88.332 3945 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1322 helix: 0.29 (0.17), residues: 833 sheet: -2.85 (0.44), residues: 84 loop : -2.05 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.003 0.001 HIS D 330 PHE 0.012 0.001 PHE A 92 TYR 0.011 0.001 TYR F 190 ARG 0.002 0.000 ARG F 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7945 (m-90) cc_final: 0.7212 (t-100) REVERT: A 131 LEU cc_start: 0.9711 (mm) cc_final: 0.9365 (pp) REVERT: A 158 MET cc_start: 0.9212 (ppp) cc_final: 0.9004 (ppp) REVERT: A 191 GLU cc_start: 0.9306 (tt0) cc_final: 0.9081 (pp20) REVERT: A 400 MET cc_start: 0.9222 (mmm) cc_final: 0.8813 (tpp) REVERT: C 43 ASP cc_start: 0.9311 (p0) cc_final: 0.9044 (p0) REVERT: C 46 GLU cc_start: 0.9278 (tt0) cc_final: 0.8797 (pt0) REVERT: E 81 MET cc_start: 0.8987 (ttm) cc_final: 0.8682 (tpp) REVERT: E 121 TYR cc_start: 0.8786 (t80) cc_final: 0.8499 (t80) REVERT: E 141 ILE cc_start: 0.9618 (mm) cc_final: 0.9387 (tp) REVERT: F 66 MET cc_start: 0.9593 (mmm) cc_final: 0.9334 (mmm) REVERT: F 87 MET cc_start: 0.9481 (ttp) cc_final: 0.9064 (tmm) REVERT: F 101 GLN cc_start: 0.8733 (tt0) cc_final: 0.8382 (mt0) REVERT: F 107 PHE cc_start: 0.8621 (t80) cc_final: 0.8220 (t80) REVERT: F 128 ASP cc_start: 0.9128 (m-30) cc_final: 0.8846 (m-30) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2200 time to fit residues: 42.6032 Evaluate side-chains 81 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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: 10.0000 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 290 ASN A 347 GLN A 394 GLN A 398 GLN D 288 HIS D 307 GLN D 334 HIS D 494 GLN D 558 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.045918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.034771 restraints weight = 78555.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.035746 restraints weight = 42961.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.036400 restraints weight = 28829.926| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 10961 Z= 0.451 Angle : 0.741 14.577 14873 Z= 0.366 Chirality : 0.043 0.181 1777 Planarity : 0.004 0.035 1855 Dihedral : 3.697 18.633 1480 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.25 % Allowed : 12.51 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1322 helix: 1.35 (0.18), residues: 827 sheet: -2.35 (0.45), residues: 90 loop : -1.41 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 513 HIS 0.012 0.002 HIS D 334 PHE 0.026 0.002 PHE B 64 TYR 0.016 0.002 TYR A 139 ARG 0.004 0.001 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9196 (tp) cc_final: 0.8996 (tt) REVERT: A 65 TRP cc_start: 0.8311 (m-90) cc_final: 0.7303 (t-100) REVERT: A 158 MET cc_start: 0.9103 (ppp) cc_final: 0.8872 (ppp) REVERT: A 290 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8262 (t0) REVERT: A 337 MET cc_start: 0.8839 (mpp) cc_final: 0.8622 (pmm) REVERT: B 58 LEU cc_start: 0.8971 (tt) cc_final: 0.8763 (tt) REVERT: B 59 PHE cc_start: 0.8630 (m-10) cc_final: 0.7478 (t80) REVERT: D 491 MET cc_start: 0.8981 (tmm) cc_final: 0.8456 (tpp) REVERT: D 608 MET cc_start: 0.9522 (mtm) cc_final: 0.9192 (mtm) REVERT: E 121 TYR cc_start: 0.9109 (t80) cc_final: 0.8760 (t80) REVERT: E 165 MET cc_start: 0.8725 (ttp) cc_final: 0.8393 (ppp) REVERT: E 200 ASN cc_start: 0.9594 (t0) cc_final: 0.9358 (t0) REVERT: F 66 MET cc_start: 0.9672 (mmm) cc_final: 0.9421 (mmm) REVERT: F 87 MET cc_start: 0.9373 (ttp) cc_final: 0.8957 (tmm) REVERT: F 114 ASP cc_start: 0.9235 (OUTLIER) cc_final: 0.8992 (p0) outliers start: 14 outliers final: 7 residues processed: 84 average time/residue: 0.1954 time to fit residues: 26.2571 Evaluate side-chains 72 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 114 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 135 optimal weight: 40.0000 chunk 4 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 290 ASN D 282 HIS D 330 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.047400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.036185 restraints weight = 76729.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.037226 restraints weight = 42036.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.037812 restraints weight = 28153.563| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10961 Z= 0.154 Angle : 0.549 13.493 14873 Z= 0.265 Chirality : 0.039 0.221 1777 Planarity : 0.003 0.036 1855 Dihedral : 3.357 17.170 1480 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.52 % Allowed : 13.40 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1322 helix: 1.78 (0.18), residues: 841 sheet: -1.96 (0.47), residues: 90 loop : -1.12 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.003 0.001 HIS D 309 PHE 0.018 0.001 PHE B 66 TYR 0.011 0.001 TYR F 190 ARG 0.002 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8304 (m-90) cc_final: 0.7277 (t-100) REVERT: A 158 MET cc_start: 0.9112 (ppp) cc_final: 0.8876 (ppp) REVERT: A 337 MET cc_start: 0.8792 (mpp) cc_final: 0.8541 (pmm) REVERT: A 450 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9293 (mp) REVERT: E 121 TYR cc_start: 0.8968 (t80) cc_final: 0.8668 (t80) REVERT: F 66 MET cc_start: 0.9638 (mmm) cc_final: 0.9367 (mmp) REVERT: F 87 MET cc_start: 0.9371 (ttp) cc_final: 0.8925 (tmm) outliers start: 17 outliers final: 8 residues processed: 90 average time/residue: 0.1708 time to fit residues: 24.8765 Evaluate side-chains 72 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 201 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 66 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.047547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.036311 restraints weight = 76415.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.037331 restraints weight = 41254.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.038086 restraints weight = 27739.807| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10961 Z= 0.156 Angle : 0.541 12.055 14873 Z= 0.259 Chirality : 0.039 0.228 1777 Planarity : 0.003 0.038 1855 Dihedral : 3.234 20.208 1480 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.52 % Allowed : 14.92 % Favored : 83.56 % 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: 1.41 (0.24), residues: 1322 helix: 2.02 (0.18), residues: 840 sheet: -1.40 (0.49), residues: 88 loop : -0.87 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.003 0.001 HIS D 330 PHE 0.012 0.001 PHE A 254 TYR 0.010 0.001 TYR F 190 ARG 0.004 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8297 (m-90) cc_final: 0.7310 (t-100) REVERT: A 131 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9315 (pp) REVERT: A 158 MET cc_start: 0.9157 (ppp) cc_final: 0.8919 (ppp) REVERT: A 337 MET cc_start: 0.8842 (mpp) cc_final: 0.8585 (pmm) REVERT: A 400 MET cc_start: 0.9046 (tpp) cc_final: 0.8753 (tpp) REVERT: C 36 LEU cc_start: 0.9548 (mt) cc_final: 0.9335 (pp) REVERT: E 81 MET cc_start: 0.9080 (ttm) cc_final: 0.8610 (tpp) REVERT: E 121 TYR cc_start: 0.8936 (t80) cc_final: 0.8670 (t80) REVERT: E 165 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8351 (ppp) REVERT: F 66 MET cc_start: 0.9620 (mmm) cc_final: 0.9379 (mmp) REVERT: F 108 MET cc_start: 0.9302 (mpp) cc_final: 0.8930 (mpp) REVERT: F 128 ASP cc_start: 0.9170 (m-30) cc_final: 0.8945 (m-30) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.1778 time to fit residues: 23.3170 Evaluate side-chains 76 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 201 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.036310 restraints weight = 76827.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.037352 restraints weight = 41353.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.038089 restraints weight = 27475.192| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10961 Z= 0.162 Angle : 0.531 11.590 14873 Z= 0.256 Chirality : 0.038 0.242 1777 Planarity : 0.003 0.040 1855 Dihedral : 3.173 18.519 1480 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.59 % Allowed : 14.39 % Favored : 83.02 % 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: 1.62 (0.24), residues: 1322 helix: 2.13 (0.18), residues: 842 sheet: -1.20 (0.50), residues: 88 loop : -0.73 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 95 HIS 0.003 0.001 HIS D 330 PHE 0.022 0.001 PHE B 64 TYR 0.011 0.001 TYR F 190 ARG 0.004 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8431 (m-90) cc_final: 0.7339 (t-100) REVERT: A 131 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9290 (pp) REVERT: A 158 MET cc_start: 0.9172 (ppp) cc_final: 0.8918 (ppp) REVERT: A 244 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7938 (pmm) REVERT: A 337 MET cc_start: 0.8844 (mpp) cc_final: 0.8579 (pmm) REVERT: A 400 MET cc_start: 0.9012 (tpp) cc_final: 0.8737 (tpp) REVERT: A 450 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9249 (mp) REVERT: C 36 LEU cc_start: 0.9549 (mt) cc_final: 0.9320 (pp) REVERT: E 81 MET cc_start: 0.9072 (ttm) cc_final: 0.8626 (tpp) REVERT: E 121 TYR cc_start: 0.8921 (t80) cc_final: 0.8627 (t80) REVERT: E 165 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8370 (ppp) REVERT: E 186 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8969 (ttm170) REVERT: F 66 MET cc_start: 0.9619 (mmm) cc_final: 0.9384 (mmp) REVERT: F 87 MET cc_start: 0.9367 (ttp) cc_final: 0.8991 (tmm) REVERT: F 108 MET cc_start: 0.9311 (mpp) cc_final: 0.8893 (mmm) outliers start: 29 outliers final: 15 residues processed: 88 average time/residue: 0.1997 time to fit residues: 27.4214 Evaluate side-chains 87 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 186 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 102 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** E 173 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 = 0.3093 r_free = 0.3093 target = 0.047247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.036120 restraints weight = 77571.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.037153 restraints weight = 42279.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.037840 restraints weight = 28310.583| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10961 Z= 0.179 Angle : 0.548 11.247 14873 Z= 0.264 Chirality : 0.039 0.253 1777 Planarity : 0.003 0.040 1855 Dihedral : 3.186 19.161 1480 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.68 % Allowed : 15.37 % Favored : 81.95 % 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: 1.75 (0.24), residues: 1322 helix: 2.19 (0.18), residues: 846 sheet: -1.09 (0.51), residues: 88 loop : -0.61 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 95 HIS 0.003 0.001 HIS D 330 PHE 0.023 0.001 PHE B 64 TYR 0.011 0.001 TYR F 190 ARG 0.006 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8503 (m-90) cc_final: 0.7397 (t-100) REVERT: A 158 MET cc_start: 0.9183 (ppp) cc_final: 0.8921 (ppp) REVERT: A 165 MET cc_start: 0.9501 (ppp) cc_final: 0.9119 (tmm) REVERT: A 337 MET cc_start: 0.8867 (mpp) cc_final: 0.8595 (pmm) REVERT: A 400 MET cc_start: 0.9011 (tpp) cc_final: 0.8655 (tpp) REVERT: C 36 LEU cc_start: 0.9553 (mt) cc_final: 0.9327 (pp) REVERT: E 81 MET cc_start: 0.9052 (ttm) cc_final: 0.8622 (tpp) REVERT: E 121 TYR cc_start: 0.8951 (t80) cc_final: 0.8627 (t80) REVERT: E 165 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8385 (ppp) REVERT: E 186 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.9067 (ttm170) REVERT: F 66 MET cc_start: 0.9621 (mmm) cc_final: 0.9371 (mmp) REVERT: F 108 MET cc_start: 0.9338 (mpp) cc_final: 0.8937 (mmm) outliers start: 30 outliers final: 14 residues processed: 91 average time/residue: 0.1901 time to fit residues: 26.9239 Evaluate side-chains 82 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 186 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 11 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: A 156 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 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 = 0.3076 r_free = 0.3076 target = 0.046642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.035501 restraints weight = 79025.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.036507 restraints weight = 43346.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.037185 restraints weight = 29077.832| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10961 Z= 0.247 Angle : 0.607 13.536 14873 Z= 0.292 Chirality : 0.040 0.252 1777 Planarity : 0.003 0.040 1855 Dihedral : 3.317 19.862 1480 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.23 % Allowed : 16.35 % Favored : 81.41 % 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: 1.77 (0.24), residues: 1322 helix: 2.17 (0.18), residues: 844 sheet: -1.03 (0.52), residues: 88 loop : -0.49 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 95 HIS 0.003 0.001 HIS D 390 PHE 0.019 0.001 PHE B 64 TYR 0.013 0.001 TYR F 190 ARG 0.003 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8470 (m-90) cc_final: 0.7548 (t-100) REVERT: A 158 MET cc_start: 0.9172 (ppp) cc_final: 0.8960 (ppp) REVERT: A 165 MET cc_start: 0.9535 (ppp) cc_final: 0.9133 (tmm) REVERT: A 337 MET cc_start: 0.8903 (mpp) cc_final: 0.8632 (pmm) REVERT: B 59 PHE cc_start: 0.8615 (m-10) cc_final: 0.7309 (t80) REVERT: E 81 MET cc_start: 0.9052 (ttm) cc_final: 0.8591 (tpp) REVERT: E 121 TYR cc_start: 0.8994 (t80) cc_final: 0.8664 (t80) REVERT: E 165 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8443 (ppp) REVERT: F 87 MET cc_start: 0.9398 (ttp) cc_final: 0.9034 (tmm) REVERT: F 108 MET cc_start: 0.9350 (mpp) cc_final: 0.8945 (mmm) REVERT: F 113 ILE cc_start: 0.9655 (OUTLIER) cc_final: 0.9261 (mt) REVERT: F 128 ASP cc_start: 0.9182 (m-30) cc_final: 0.8912 (p0) outliers start: 25 outliers final: 15 residues processed: 85 average time/residue: 0.1966 time to fit residues: 26.0300 Evaluate side-chains 81 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain F residue 113 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 86 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.0010 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 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 = 0.3081 r_free = 0.3081 target = 0.046811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.035709 restraints weight = 77607.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.036676 restraints weight = 42704.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.037388 restraints weight = 29030.262| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10961 Z= 0.207 Angle : 0.623 12.586 14873 Z= 0.291 Chirality : 0.040 0.282 1777 Planarity : 0.003 0.039 1855 Dihedral : 3.284 19.179 1480 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.79 % Allowed : 16.98 % Favored : 81.23 % 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: 1.75 (0.24), residues: 1322 helix: 2.13 (0.18), residues: 849 sheet: -0.94 (0.53), residues: 88 loop : -0.51 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 95 HIS 0.003 0.001 HIS D 330 PHE 0.018 0.001 PHE B 64 TYR 0.012 0.001 TYR F 190 ARG 0.004 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8474 (m-90) cc_final: 0.7484 (t-100) REVERT: A 158 MET cc_start: 0.9168 (ppp) cc_final: 0.8946 (ppp) REVERT: A 165 MET cc_start: 0.9520 (ppp) cc_final: 0.9134 (ppp) REVERT: A 337 MET cc_start: 0.8913 (mpp) cc_final: 0.8569 (pmm) REVERT: E 81 MET cc_start: 0.9018 (ttm) cc_final: 0.8517 (tpp) REVERT: E 121 TYR cc_start: 0.8997 (t80) cc_final: 0.8718 (t80) REVERT: E 165 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8422 (ppp) REVERT: F 66 MET cc_start: 0.9122 (mmm) cc_final: 0.8850 (mmp) REVERT: F 87 MET cc_start: 0.9380 (ttp) cc_final: 0.9008 (tmm) REVERT: F 108 MET cc_start: 0.9374 (mpp) cc_final: 0.8984 (mmm) outliers start: 20 outliers final: 16 residues processed: 79 average time/residue: 0.2069 time to fit residues: 25.7039 Evaluate side-chains 77 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 186 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 107 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS D 539 ASN ** E 173 ASN ** 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 = 0.3066 r_free = 0.3066 target = 0.046377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.035322 restraints weight = 78088.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.036309 restraints weight = 42872.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.037006 restraints weight = 28769.002| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10961 Z= 0.250 Angle : 0.649 12.115 14873 Z= 0.306 Chirality : 0.042 0.389 1777 Planarity : 0.003 0.042 1855 Dihedral : 3.380 18.904 1480 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.88 % Allowed : 16.89 % Favored : 81.23 % 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: 1.77 (0.24), residues: 1322 helix: 2.15 (0.18), residues: 844 sheet: -0.83 (0.54), residues: 88 loop : -0.50 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 95 HIS 0.004 0.001 HIS F 106 PHE 0.017 0.001 PHE B 64 TYR 0.013 0.001 TYR F 190 ARG 0.004 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8525 (m-90) cc_final: 0.7523 (t-100) REVERT: A 158 MET cc_start: 0.9174 (ppp) cc_final: 0.8948 (ppp) REVERT: A 165 MET cc_start: 0.9518 (ppp) cc_final: 0.9122 (ppp) REVERT: A 337 MET cc_start: 0.8941 (mpp) cc_final: 0.8594 (pmm) REVERT: A 400 MET cc_start: 0.9042 (tpp) cc_final: 0.8750 (tpp) REVERT: B 59 PHE cc_start: 0.8632 (m-10) cc_final: 0.7376 (t80) REVERT: B 60 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9307 (pp) REVERT: E 121 TYR cc_start: 0.9010 (t80) cc_final: 0.8707 (t80) REVERT: E 165 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8491 (ppp) REVERT: F 66 MET cc_start: 0.9156 (mmm) cc_final: 0.8918 (mmm) REVERT: F 108 MET cc_start: 0.9364 (mpp) cc_final: 0.8812 (mtt) outliers start: 21 outliers final: 15 residues processed: 78 average time/residue: 0.2139 time to fit residues: 26.0730 Evaluate side-chains 78 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 201 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 77 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 48 optimal weight: 0.0270 chunk 38 optimal weight: 1.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 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 = 0.3094 r_free = 0.3094 target = 0.047253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.036259 restraints weight = 77134.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.037228 restraints weight = 43230.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.037919 restraints weight = 29489.315| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10961 Z= 0.163 Angle : 0.628 14.621 14873 Z= 0.288 Chirality : 0.041 0.348 1777 Planarity : 0.003 0.041 1855 Dihedral : 3.266 18.916 1480 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.07 % Allowed : 17.96 % Favored : 80.97 % 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: 1.85 (0.24), residues: 1322 helix: 2.16 (0.18), residues: 850 sheet: -0.73 (0.54), residues: 88 loop : -0.39 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 14 HIS 0.004 0.001 HIS D 330 PHE 0.017 0.001 PHE B 64 TYR 0.010 0.001 TYR F 190 ARG 0.005 0.000 ARG F 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8474 (m-90) cc_final: 0.7517 (t-100) REVERT: A 158 MET cc_start: 0.9107 (ppp) cc_final: 0.8864 (ppp) REVERT: A 165 MET cc_start: 0.9477 (ppp) cc_final: 0.9072 (ppp) REVERT: A 191 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8429 (tm-30) REVERT: A 337 MET cc_start: 0.8900 (mpp) cc_final: 0.8524 (pmm) REVERT: A 400 MET cc_start: 0.9023 (tpp) cc_final: 0.8720 (tpp) REVERT: E 121 TYR cc_start: 0.8876 (t80) cc_final: 0.8613 (t80) REVERT: E 165 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8448 (ppp) REVERT: F 108 MET cc_start: 0.9314 (mpp) cc_final: 0.8961 (mmm) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.1814 time to fit residues: 22.4118 Evaluate side-chains 74 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 171 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 67 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 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 = 0.3073 r_free = 0.3073 target = 0.046574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.035556 restraints weight = 77067.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.036521 restraints weight = 42276.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.037231 restraints weight = 28509.182| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10961 Z= 0.241 Angle : 0.660 14.422 14873 Z= 0.308 Chirality : 0.041 0.339 1777 Planarity : 0.003 0.042 1855 Dihedral : 3.306 18.477 1480 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.25 % Allowed : 18.41 % Favored : 80.34 % 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: 1.84 (0.24), residues: 1322 helix: 2.18 (0.18), residues: 844 sheet: -0.76 (0.55), residues: 88 loop : -0.42 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 95 HIS 0.003 0.001 HIS F 106 PHE 0.022 0.001 PHE B 66 TYR 0.012 0.001 TYR F 190 ARG 0.005 0.000 ARG F 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2776.14 seconds wall clock time: 51 minutes 5.81 seconds (3065.81 seconds total)