Starting phenix.real_space_refine on Thu Nov 14 20:52:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ida_35361/11_2024/8ida_35361_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ida_35361/11_2024/8ida_35361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ida_35361/11_2024/8ida_35361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ida_35361/11_2024/8ida_35361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ida_35361/11_2024/8ida_35361_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ida_35361/11_2024/8ida_35361_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 27 5.16 5 C 4816 2.51 5 N 1189 2.21 5 O 1340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7372 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3661 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 22, 'TRANS': 447} Chain: "B" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3586 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 4.79, per 1000 atoms: 0.65 Number of scatterers: 7372 At special positions: 0 Unit cell: (97.83, 81.525, 129.353, 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 27 16.00 O 1340 8.00 N 1189 7.00 C 4816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 60.4% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.704A pdb=" N GLY A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 207 removed outlier: 4.101A pdb=" N ARG A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.689A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 235' Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.624A pdb=" N ARG A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TYR A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.575A pdb=" N GLN A 275 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 323 through 342 removed outlier: 4.196A pdb=" N VAL A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.565A pdb=" N ASN A 353 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.765A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.547A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 509 through 516 removed outlier: 3.790A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.765A pdb=" N SER A 589 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 80 removed outlier: 3.536A pdb=" N VAL B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 81 through 110 Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 125 through 139 removed outlier: 4.004A pdb=" N ALA B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 157 Processing helix chain 'B' and resid 167 through 189 removed outlier: 4.042A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 221 removed outlier: 3.522A pdb=" N LYS B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 removed outlier: 5.336A pdb=" N LEU B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 removed outlier: 3.708A pdb=" N THR B 264 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 298 Proline residue: B 275 - end of helix removed outlier: 3.664A pdb=" N ILE B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 356 removed outlier: 4.042A pdb=" N THR B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 392 through 400 removed outlier: 4.250A pdb=" N VAL B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASN B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 422 Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.708A pdb=" N PHE B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.757A pdb=" N CYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 476 removed outlier: 3.633A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 501 removed outlier: 3.599A pdb=" N LEU B 486 " --> pdb=" O PRO B 482 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.857A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR A 226 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU A 225 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N CYS A 432 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL A 466 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP A 434 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N SER A 468 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.327A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 621 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA5, first strand: chain 'B' and resid 365 through 366 393 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2250 1.34 - 1.46: 1279 1.46 - 1.58: 3984 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 7553 Sorted by residual: bond pdb=" CA TYR B 601 " pdb=" C TYR B 601 " ideal model delta sigma weight residual 1.525 1.489 0.036 2.10e-02 2.27e+03 2.87e+00 bond pdb=" CA TYR B 601 " pdb=" CB TYR B 601 " ideal model delta sigma weight residual 1.530 1.497 0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" N TYR B 601 " pdb=" CA TYR B 601 " ideal model delta sigma weight residual 1.458 1.427 0.031 1.90e-02 2.77e+03 2.67e+00 bond pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sigma weight residual 1.409 1.440 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C3 NAG D 1 " pdb=" O3 NAG D 1 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 7548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 10072 1.86 - 3.72: 169 3.72 - 5.58: 36 5.58 - 7.44: 5 7.44 - 9.31: 4 Bond angle restraints: 10286 Sorted by residual: angle pdb=" CA TYR B 601 " pdb=" CB TYR B 601 " pdb=" CG TYR B 601 " ideal model delta sigma weight residual 113.90 105.26 8.64 1.80e+00 3.09e-01 2.31e+01 angle pdb=" C ASP B 228 " pdb=" N PRO B 229 " pdb=" CA PRO B 229 " ideal model delta sigma weight residual 121.65 117.26 4.39 1.01e+00 9.80e-01 1.89e+01 angle pdb=" N GLY B 222 " pdb=" CA GLY B 222 " pdb=" C GLY B 222 " ideal model delta sigma weight residual 110.20 115.03 -4.83 1.32e+00 5.74e-01 1.34e+01 angle pdb=" N ARG B 421 " pdb=" CA ARG B 421 " pdb=" C ARG B 421 " ideal model delta sigma weight residual 112.23 116.66 -4.43 1.26e+00 6.30e-01 1.23e+01 angle pdb=" CA PRO A 602 " pdb=" N PRO A 602 " pdb=" CD PRO A 602 " ideal model delta sigma weight residual 112.00 107.43 4.57 1.40e+00 5.10e-01 1.07e+01 ... (remaining 10281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.68: 4197 25.68 - 51.37: 240 51.37 - 77.05: 40 77.05 - 102.74: 25 102.74 - 128.42: 26 Dihedral angle restraints: 4528 sinusoidal: 1848 harmonic: 2680 Sorted by residual: dihedral pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " pdb=" C5 NAG D 2 " ideal model delta sinusoidal sigma weight residual -62.96 65.46 -128.42 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C2 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" O4 NAG E 1 " ideal model delta sinusoidal sigma weight residual 175.11 58.60 116.51 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" O3 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" O4 NAG E 1 " ideal model delta sinusoidal sigma weight residual 295.45 178.97 116.48 1 3.00e+01 1.11e-03 1.54e+01 ... (remaining 4525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.263: 1211 0.263 - 0.525: 2 0.525 - 0.788: 1 0.788 - 1.050: 0 1.050 - 1.313: 1 Chirality restraints: 1215 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.02e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.09 -1.31 2.00e-01 2.50e+01 4.31e+01 ... (remaining 1212 not shown) Planarity restraints: 1277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.358 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG E 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.041 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.531 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.344 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG D 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.515 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.336 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG F 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.511 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.095 2.00e-02 2.50e+03 ... (remaining 1274 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1230 2.76 - 3.30: 7173 3.30 - 3.83: 12087 3.83 - 4.37: 13466 4.37 - 4.90: 23897 Nonbonded interactions: 57853 Sorted by model distance: nonbonded pdb=" OG SER B 81 " pdb=" O ASN B 230 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR A 469 " pdb=" O PRO A 488 " model vdw 2.243 3.040 nonbonded pdb=" NH2 ARG A 604 " pdb=" O LYS A 616 " model vdw 2.250 3.120 nonbonded pdb=" O VAL B 224 " pdb=" ND2 ASN B 226 " model vdw 2.278 3.120 nonbonded pdb=" OG1 THR A 460 " pdb=" OH TYR A 554 " model vdw 2.302 3.040 ... (remaining 57848 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.640 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 0.062 7553 Z= 0.204 Angle : 0.617 9.305 10286 Z= 0.308 Chirality : 0.060 1.313 1215 Planarity : 0.021 0.306 1273 Dihedral : 20.753 128.423 2803 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.38 % Allowed : 0.25 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.28), residues: 930 helix: 1.94 (0.23), residues: 491 sheet: 0.17 (0.65), residues: 64 loop : -1.14 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 338 HIS 0.001 0.000 HIS B 420 PHE 0.016 0.001 PHE B 233 TYR 0.007 0.001 TYR B 259 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.846 Fit side-chains REVERT: A 319 TRP cc_start: 0.6455 (m100) cc_final: 0.5888 (m100) REVERT: B 78 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7936 (tp30) REVERT: B 158 LYS cc_start: 0.8849 (tppt) cc_final: 0.8635 (tptt) outliers start: 3 outliers final: 0 residues processed: 89 average time/residue: 0.1690 time to fit residues: 21.5011 Evaluate side-chains 66 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.0070 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7553 Z= 0.185 Angle : 0.622 9.358 10286 Z= 0.288 Chirality : 0.044 0.369 1215 Planarity : 0.004 0.034 1273 Dihedral : 19.752 104.283 1159 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.39 % Allowed : 7.10 % Favored : 91.51 % 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: 1.26 (0.28), residues: 930 helix: 2.23 (0.23), residues: 501 sheet: 0.14 (0.63), residues: 64 loop : -1.06 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.002 0.001 HIS B 319 PHE 0.011 0.001 PHE B 200 TYR 0.007 0.001 TYR B 259 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.823 Fit side-chains REVERT: A 249 LEU cc_start: 0.7767 (tt) cc_final: 0.7529 (tt) REVERT: A 319 TRP cc_start: 0.6416 (m100) cc_final: 0.5926 (m100) REVERT: B 78 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7967 (tp30) REVERT: B 233 PHE cc_start: 0.7032 (t80) cc_final: 0.6784 (t80) REVERT: B 432 ASN cc_start: 0.7263 (m-40) cc_final: 0.6972 (t0) outliers start: 11 outliers final: 10 residues processed: 80 average time/residue: 0.1505 time to fit residues: 18.1036 Evaluate side-chains 76 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 75 optimal weight: 0.0770 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7553 Z= 0.214 Angle : 0.609 7.419 10286 Z= 0.283 Chirality : 0.043 0.315 1215 Planarity : 0.003 0.034 1273 Dihedral : 15.478 105.236 1159 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.28 % Allowed : 8.62 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.28), residues: 930 helix: 2.40 (0.23), residues: 498 sheet: 0.19 (0.64), residues: 64 loop : -1.07 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.003 0.001 HIS B 319 PHE 0.013 0.001 PHE B 216 TYR 0.009 0.001 TYR B 146 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.014 Fit side-chains REVERT: A 319 TRP cc_start: 0.6547 (m100) cc_final: 0.6068 (m100) REVERT: B 78 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7997 (tp30) REVERT: B 432 ASN cc_start: 0.7279 (m-40) cc_final: 0.6976 (t0) outliers start: 18 outliers final: 14 residues processed: 90 average time/residue: 0.1814 time to fit residues: 23.3045 Evaluate side-chains 80 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7553 Z= 0.216 Angle : 0.613 10.971 10286 Z= 0.281 Chirality : 0.043 0.264 1215 Planarity : 0.003 0.031 1273 Dihedral : 13.548 104.247 1159 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.66 % Allowed : 10.39 % Favored : 86.95 % 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: 1.35 (0.28), residues: 930 helix: 2.37 (0.23), residues: 501 sheet: 0.14 (0.64), residues: 66 loop : -1.15 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 319 PHE 0.013 0.001 PHE B 200 TYR 0.008 0.001 TYR A 454 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.882 Fit side-chains REVERT: A 252 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8072 (mp) REVERT: A 363 GLU cc_start: 0.8314 (tt0) cc_final: 0.8109 (tt0) REVERT: B 432 ASN cc_start: 0.7288 (m-40) cc_final: 0.6974 (t0) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 0.1590 time to fit residues: 20.1496 Evaluate side-chains 78 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7553 Z= 0.249 Angle : 0.625 10.223 10286 Z= 0.288 Chirality : 0.043 0.265 1215 Planarity : 0.003 0.031 1273 Dihedral : 11.990 106.148 1159 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.53 % Allowed : 12.29 % Favored : 85.17 % 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 (0.28), residues: 930 helix: 2.31 (0.23), residues: 501 sheet: 0.10 (0.64), residues: 66 loop : -1.15 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 319 PHE 0.015 0.001 PHE B 216 TYR 0.009 0.001 TYR A 454 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.909 Fit side-chains REVERT: A 363 GLU cc_start: 0.8352 (tt0) cc_final: 0.8118 (tt0) REVERT: B 432 ASN cc_start: 0.7300 (m-40) cc_final: 0.6976 (t0) outliers start: 20 outliers final: 18 residues processed: 78 average time/residue: 0.1759 time to fit residues: 20.0131 Evaluate side-chains 79 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7553 Z= 0.206 Angle : 0.611 8.729 10286 Z= 0.281 Chirality : 0.042 0.241 1215 Planarity : 0.003 0.032 1273 Dihedral : 11.160 106.790 1159 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.41 % Allowed : 12.93 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.28), residues: 930 helix: 2.32 (0.23), residues: 501 sheet: 0.12 (0.64), residues: 66 loop : -1.11 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 319 PHE 0.012 0.001 PHE B 200 TYR 0.008 0.001 TYR A 313 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.927 Fit side-chains outliers start: 19 outliers final: 18 residues processed: 78 average time/residue: 0.1676 time to fit residues: 19.6366 Evaluate side-chains 79 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.0050 chunk 89 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7553 Z= 0.180 Angle : 0.603 9.989 10286 Z= 0.275 Chirality : 0.042 0.270 1215 Planarity : 0.003 0.032 1273 Dihedral : 10.449 107.066 1159 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.53 % Allowed : 13.18 % Favored : 84.28 % 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: 1.35 (0.28), residues: 930 helix: 2.32 (0.24), residues: 501 sheet: 0.22 (0.65), residues: 66 loop : -1.07 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.001 0.001 HIS B 319 PHE 0.011 0.001 PHE B 200 TYR 0.008 0.001 TYR A 313 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.830 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 19 residues processed: 77 average time/residue: 0.1690 time to fit residues: 19.4186 Evaluate side-chains 79 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 451 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 85 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7553 Z= 0.188 Angle : 0.588 7.570 10286 Z= 0.272 Chirality : 0.042 0.292 1215 Planarity : 0.003 0.032 1273 Dihedral : 9.784 106.995 1159 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.28 % Allowed : 13.69 % Favored : 84.03 % 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 (0.28), residues: 930 helix: 2.37 (0.24), residues: 498 sheet: 0.18 (0.64), residues: 66 loop : -1.01 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS A 539 PHE 0.012 0.001 PHE B 200 TYR 0.008 0.001 TYR B 146 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.804 Fit side-chains outliers start: 18 outliers final: 16 residues processed: 77 average time/residue: 0.1532 time to fit residues: 18.1672 Evaluate side-chains 76 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 0.0030 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7553 Z= 0.189 Angle : 0.573 7.874 10286 Z= 0.269 Chirality : 0.041 0.241 1215 Planarity : 0.003 0.032 1273 Dihedral : 9.136 106.787 1159 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.15 % Allowed : 14.07 % Favored : 83.78 % 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: 1.40 (0.29), residues: 930 helix: 2.34 (0.24), residues: 498 sheet: 0.17 (0.64), residues: 66 loop : -0.98 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.001 0.000 HIS A 539 PHE 0.022 0.001 PHE B 216 TYR 0.009 0.001 TYR A 313 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.876 Fit side-chains outliers start: 17 outliers final: 16 residues processed: 77 average time/residue: 0.1604 time to fit residues: 18.5440 Evaluate side-chains 75 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7553 Z= 0.161 Angle : 0.567 7.574 10286 Z= 0.265 Chirality : 0.041 0.251 1215 Planarity : 0.003 0.032 1273 Dihedral : 8.766 106.860 1159 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.15 % Allowed : 14.32 % Favored : 83.52 % 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: 1.47 (0.29), residues: 930 helix: 2.40 (0.24), residues: 498 sheet: 0.21 (0.64), residues: 66 loop : -0.95 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.001 0.001 HIS A 539 PHE 0.018 0.001 PHE B 216 TYR 0.009 0.001 TYR A 313 ARG 0.003 0.000 ARG A 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.782 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 75 average time/residue: 0.1592 time to fit residues: 17.7919 Evaluate side-chains 76 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 0.0570 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093063 restraints weight = 11352.886| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.78 r_work: 0.2959 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7553 Z= 0.169 Angle : 0.567 7.692 10286 Z= 0.266 Chirality : 0.041 0.249 1215 Planarity : 0.003 0.032 1273 Dihedral : 8.374 106.325 1159 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.90 % Allowed : 14.58 % Favored : 83.52 % 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: 1.50 (0.29), residues: 930 helix: 2.43 (0.24), residues: 498 sheet: 0.22 (0.64), residues: 66 loop : -0.95 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 319 HIS 0.001 0.000 HIS B 367 PHE 0.018 0.001 PHE B 216 TYR 0.009 0.001 TYR A 313 ARG 0.004 0.000 ARG A 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1590.46 seconds wall clock time: 29 minutes 49.49 seconds (1789.49 seconds total)